E: Could not open file /var/lib/dpkg/status

Sam_ suggests this article as an answer to your question:

sudo mv /var/lib/dpkg/status-bad /var/lib/dpkg/status
sudo apt-get clean && sudo apt-get autoremove

FAQ #1591: “'E:Encountered a section with no Package: header, E:Problem with MergeList”.

Sorry, this did resolve the problem

You mean *not*?

Please post output of cmd in #1, thanks.

Sorry Sam I meant "Sorry, this did not resolve the problem"

I assume you did not mean:

lee@lee-linux:~$ cmd
No command 'cmd' found, did you mean:
 Command 'dcmd' from package 'devscripts' (main)
 Command 'wmd' from package 'wml' (universe)
 Command 'amd' from package 'am-utils' (universe)
 Command 'tcmd' from package 'tcm' (universe)
 Command 'cme' from package 'libconfig-model-perl' (universe)
 Command 'cmp' from package 'diffutils' (main)
 Command 'qcmd' from package 'renameutils' (universe)
 Command 'mmd' from package 'mtools' (main)
 Command 'cm' from package 'config-manager' (universe)
 Command 'mcd' from package 'mtools' (main)
 Command 'icmd' from package 'renameutils' (universe)
 Command 'cad' from package 'rheolef' (universe)
cmd: command not found

lee@lee-linux:~$ sudo mv /var/lib/dpkg/status-bad /var/lib/dpkg/status
[sudo] password for lee:
mv: cannot stat `/var/lib/dpkg/status-bad': No such file or directory
lee@lee-linux:~$ sudo apt-get clean && sudo apt-get autoremove
Reading package lists... Done
Building dependency tree
Reading state information... Done
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
lee@lee-linux:~$ sudo rm -rf /var/lib/apt/lists
lee@lee-linux:~$ sudo mkdir /var/lib/apt/lists
lee@lee-linux:~$ sudo mkdir /var/lib/apt/lists/partial
lee@lee-linux:~$

Thanks. Please post output of:
sudo apt-get update
sudo apt-get upgrade

lee@lee-linux:~$ sudo apt-get update
[sudo] password for lee:
Ign http://webmin.mirror.somersettechsolutions.co.uk sarge InRelease
Ign http://extras.ubuntu.com precise InRelease
Ign http://archive.ubuntu.com precise InRelease
Ign http://archive.ubuntu.com precise-updates InRelease
Ign http://archive.ubuntu.com precise-backports InRelease
Ign http://archive.ubuntu.com precise-security InRelease
Ign http://archive.ubuntu.com precise-proposed InRelease
Hit http://webmin.mirror.somersettechsolutions.co.uk sarge Release.gpg
Ign http://dl.google.com stable InRelease
Ign http://dl.google.com stable InRelease
Hit http://extras.ubuntu.com precise Release.gpg
Get:1 http://archive.ubuntu.com precise Release.gpg [198 B]
Get:2 http://archive.ubuntu.com precise-updates Release.gpg [198 B]
Get:3 http://archive.ubuntu.com precise-backports Release.gpg [198 B]
Get:4 http://archive.ubuntu.com precise-security Release.gpg [198 B]
Hit http://webmin.mirror.somersettechsolutions.co.uk sarge Release
Get:5 http://dl.google.com stable Release.gpg [198 B]
Get:6 http://archive.ubuntu.com precise-proposed Release.gpg [198 B]
Hit http://extras.ubuntu.com precise Release
Get:7 http://archive.ubuntu.com precise Release [49.6 kB]
Hit http://webmin.mirror.somersettechsolutions.co.uk sarge/contrib amd64 Packages
Hit http://extras.ubuntu.com precise/main Sources
Get:8 http://dl.google.com stable Release.gpg [198 B]
Hit http://webmin.mirror.somersettechsolutions.co.uk sarge/contrib i386 Packages
Ign http://webmin.mirror.somersettechsolutions.co.uk sarge/contrib TranslationIndex
Hit http://extras.ubuntu.com precise/main amd64 Packages
Hit http://extras.ubuntu.com precise/main i386 Packages
Get:9 http://archive.ubuntu.com precise-updates Release [49.6 kB]
Ign http://extras.ubuntu.com precise/main TranslationIndex
Get:10 http://archive.ubuntu.com precise-backports Release [49.6 kB]
Ign http://download.webmin.com sarge InRelease
Get:11 http://dl.google.com stable Release [1,347 B]
Get:12 http://archive.ubuntu.com precise-security Release [49.6 kB]
Get:13 http://archive.ubuntu.com precise-proposed Release [49.6 kB]
Get:14 http://archive.ubuntu.com precise/main Sources [934 kB]
Ign http://webmin.mirror.somersettechsolutions.co.uk sarge/contrib Translation-en_GB
Ign http://software.virtualmin.com virtualmin-precise InRelease
Ign http://webmin.mirror.somersettechsolutions.co.uk sarge/contrib Translation-en
Ign http://extras.ubuntu.com precise/main Translation-en_GB
Ign http://extras.ubuntu.com precise/main Translation-en
Hit http://download.webmin.com sarge Release.gpg
Get:15 http://archive.ubuntu.com precise/restricted Sources [5,470 B]
Get:16 http://archive.ubuntu.com precise/universe Sources [5,019 kB]
Ign http://software.virtualmin.com virtualmin-universal InRelease
Hit http://download.webmin.com sarge Release
Hit http://software.virtualmin.com virtualmin-precise Release.gpg
Hit http://software.virtualmin.com virtualmin-universal Release.gpg
Hit http://download.webmin.com sarge/contrib amd64 Packages
Hit http://software.virtualmin.com virtualmin-precise Release
Get:17 http://archive.ubuntu.com precise/multiverse Sources [155 kB]
Get:18 http://archive.ubuntu.com precise/main amd64 Packages [1,273 kB]
Hit http://download.webmin.com sarge/contrib i386 Packages
Get:19 http://archive.ubuntu.com precise/restricted amd64 Packages [8,452 B]
Get:20 http://archive.ubuntu.com precise/universe amd64 Packages [4,786 kB]
Get:21 http://dl.google.com stable Release [1,338 B]
Hit http://software.virtualmin.com virtualmin-universal Release
Get:22 http://dl.google.com stable/main amd64 Packages [1,248 B]
Ign http://download.webmin.com sarge/contrib TranslationIndex
Hit http://software.virtualmin.com virtualmin-precise/main amd64 Packages
Get:23 http://archive.ubuntu.com precise/multiverse amd64 Packages [119 kB]
Get:24 http://archive.ubuntu.com precise/main i386 Packages [1,274 kB]
Get:25 http://archive.ubuntu.com precise/restricted i386 Packages [8,431 B]
Get:26 http://archive.ubuntu.com precise/universe i386 Packages [4,796 kB]
Hit http://software.virtualmin.com virtualmin-precise/main i386 Packages
Get:27 http://archive.ubuntu.com precise/multiverse i386 Packages [121 kB]
Hit http://archive.ubuntu.com precise/main TranslationIndex
Hit http://archive.ubuntu.com precise/multiverse TranslationIndex
Hit http://archive.ubuntu.com precise/restricted TranslationIndex
Hit http://archive.ubuntu.com precise/universe TranslationIndex
Get:28 http://archive.ubuntu.com precise-updates/main Sources [127 kB]
Get:29 http://archive.ubuntu.com precise-updates/restricted Sources [1,379 B]
Get:30 http://archive.ubuntu.com precise-updates/universe Sources [33.0 kB]
Get:31 http://archive.ubuntu.com precise-updates/multiverse Sources [1,058 B]
Get:32 http://archive.ubuntu.com precise-updates/main amd64 Packages [315 kB]
Get:33 http://archive.ubuntu.com precise-updates/restricted amd64 Packages [2,417 B]
Get:34 http://archive.ubuntu.com precise-updates/universe amd64 Packages [88.1 kB]
Ign http://software.virtualmin.com virtualmin-precise/main TranslationIndex
Get:35 http://archive.ubuntu.com precise-updates/multiverse amd64 Packages [1,829 B]
Get:36 http://archive.ubuntu.com precise-updates/main i386 Packages [318 kB]
Get:37 http://archive.ubuntu.com precise-updates/restricted i386 Packages [2,439 B]
Get:38 http://archive.ubuntu.com precise-updates/universe i386 Packages [88.6 kB]
Get:39 http://archive.ubuntu.com precise-updates/multiverse i386 Packages [2,047 B]
Hit http://archive.ubuntu.com precise-updates/main TranslationIndex
Hit http://archive.ubuntu.com precise-updates/multiverse TranslationIndex
Hit http://archive.ubuntu.com precise-updates/restricted TranslationIndex
Hit http://archive.ubuntu.com precise-updates/universe TranslationIndex
Get:40 http://archive.ubuntu.com precise-backports/main Sources [1,845 B]
Get:41 http://archive.ubuntu.com precise-backports/restricted Sources [14 B]
Get:42 http://archive.ubuntu.com precise-backports/universe Sources [11.9 kB]
Get:43 http://archive.ubuntu.com precise-backports/multiverse Sources [1,383 B]
Get:44 http://archive.ubuntu.com precise-backports/main amd64 Packages [1,271 B]
Get:45 http://archive.ubuntu.com precise-backports/restricted amd64 Packages [14 B]
Get:46 http://archive.ubuntu.com precise-backports/universe amd64 Packages [10.1 kB]
Get:47 http://archive.ubuntu.com precise-backports/multiverse amd64 Packages [996 B]
Get:48 http://archive.ubuntu.com precise-backports/main i386 Packages [1,271 B]
Get:49 http://archive.ubuntu.com precise-backports/restricted i386 Packages [14 B]
Get:50 http://archive.ubuntu.com precise-backports/universe i386 Packages [10.2 kB]
Get:51 http://archive.ubuntu.com precise-backports/multiverse i386 Packages [999 B]
Hit http://archive.ubuntu.com precise-backports/main TranslationIndex
Hit http://archive.ubuntu.com precise-backports/multiverse TranslationIndex
Hit http://archive.ubuntu.com precise-backports/restricted TranslationIndex
Hit http://archive.ubuntu.com precise-backports/universe TranslationIndex
Get:52 http://archive.ubuntu.com precise-security/main Sources [23.1 kB]
Get:53 http://archive.ubuntu.com precise-security/restricted Sources [14 B]
Get:54 http://archive.ubuntu.com precise-security/universe Sources [7,832 B]
Get:55 http://archive.ubuntu.com precise-security/multiverse Sources [713 B]
Get:56 http://archive.ubuntu.com precise-security/main amd64 Packages [69.4 kB]
Get:57 http://archive.ubuntu.com precise-security/restricted amd64 Packages [14 B]
Get:58 http://archive.ubuntu.com precise-security/universe amd64 Packages [18.8 kB]
Get:59 http://archive.ubuntu.com precise-security/multiverse amd64 Packages [1,155 B]
Get:60 http://archive.ubuntu.com precise-security/main i386 Packages [71.8 kB]
Get:61 http://archive.ubuntu.com precise-security/restricted i386 Packages [14 B]
Get:62 http://archive.ubuntu.com precise-security/universe i386 Packages [19.0 kB]
Get:63 http://archive.ubuntu.com precise-security/multiverse i386 Packages [1,394 B]
Hit http://archive.ubuntu.com precise-security/main TranslationIndex
Hit http://archive.ubuntu.com precise-security/multiverse TranslationIndex
Hit http://archive.ubuntu.com precise-security/restricted TranslationIndex
Hit http://archive.ubuntu.com precise-security/universe TranslationIndex
Get:64 http://archive.ubuntu.com precise-proposed/restricted amd64 Packages [14 B]
Get:65 http://archive.ubuntu.com precise-proposed/main amd64 Packages [159 kB]
Get:66 http://archive.ubuntu.com precise-proposed/multiverse amd64 Packages [14 B]
Get:67 http://archive.ubuntu.com precise-proposed/universe amd64 Packages [20.1 kB]
Get:68 http://archive.ubuntu.com precise-proposed/restricted i386 Packages [14 B]
Get:69 http://archive.ubuntu.com precise-proposed/main i386 Packages [160 kB]
Hit http://software.virtualmin.com virtualmin-universal/main amd64 Packages
Get:70 http://archive.ubuntu.com precise-proposed/multiverse i386 Packages [14 B]
Get:71 http://archive.ubuntu.com precise-proposed/universe i386 Packages [20.1 kB]
Hit http://archive.ubuntu.com precise-proposed/main TranslationIndex
Hit http://archive.ubuntu.com precise-proposed/multiverse TranslationIndex
Hit http://archive.ubuntu.com precise-proposed/restricted TranslationIndex
Hit http://archive.ubuntu.com precise-proposed/universe TranslationIndex
Hit http://archive.ubuntu.com precise/main Translation-en_GB
Hit http://archive.ubuntu.com precise/main Translation-en
Hit http://archive.ubuntu.com precise/multiverse Translation-en_GB
Hit http://archive.ubuntu.com precise/multiverse Translation-en
Hit http://archive.ubuntu.com precise/restricted Translation-en_GB
Hit http://archive.ubuntu.com precise/restricted Translation-en
Hit http://archive.ubuntu.com precise/universe Translation-en_GB
Hit http://archive.ubuntu.com precise/universe Translation-en
Hit http://archive.ubuntu.com precise-updates/main Translation-en
Hit http://archive.ubuntu.com precise-updates/multiverse Translation-en
Hit http://archive.ubuntu.com precise-updates/restricted Translation-en
Hit http://archive.ubuntu.com precise-updates/universe Translation-en
Hit http://archive.ubuntu.com precise-backports/main Translation-en
Hit http://archive.ubuntu.com precise-backports/multiverse Translation-en
Hit http://archive.ubuntu.com precise-backports/restricted Translation-en
Hit http://archive.ubuntu.com precise-backports/universe Translation-en
Hit http://archive.ubuntu.com precise-security/main Translation-en
Hit http://archive.ubuntu.com precise-security/multiverse Translation-en
Hit http://archive.ubuntu.com precise-security/restricted Translation-en
Hit http://archive.ubuntu.com precise-security/universe Translation-en
Hit http://archive.ubuntu.com precise-proposed/main Translation-en_GB
Hit http://archive.ubuntu.com precise-proposed/main Translation-en
Hit http://archive.ubuntu.com precise-proposed/multiverse Translation-en_GB
Hit http://archive.ubuntu.com precise-proposed/multiverse Translation-en
Hit http://archive.ubuntu.com precise-proposed/restricted Translation-en_GB
Hit http://archive.ubuntu.com precise-proposed/restricted Translation-en
Hit http://archive.ubuntu.com precise-proposed/universe Translation-en_GB
Hit http://archive.ubuntu.com precise-proposed/universe Translation-en
Hit http://software.virtualmin.com virtualmin-universal/main i386 Packages
Ign http://software.virtualmin.com virtualmin-universal/main TranslationIndex
Get:72 http://dl.google.com stable/main i386 Packages [1,241 B]
Ign http://dl.google.com stable/main TranslationIndex
Get:73 http://dl.google.com stable/main amd64 Packages [469 B]
Get:74 http://dl.google.com stable/main i386 Packages [464 B]
Ign http://dl.google.com stable/main TranslationIndex
Ign http://dl.google.com stable/main Translation-en_GB
Ign http://dl.google.com stable/main Translation-en
Ign http://dl.google.com stable/main Translation-en_GB
Ign http://dl.google.com stable/main Translation-en
Ign http://download.webmin.com sarge/contrib Translation-en_GB
Ign http://download.webmin.com sarge/contrib Translation-en
Ign http://software.virtualmin.com virtualmin-precise/main Translation-en_GB
Ign http://software.virtualmin.com virtualmin-precise/main Translation-en
Ign http://software.virtualmin.com virtualmin-universal/main Translation-en_GB
Ign http://software.virtualmin.com virtualmin-universal/main Translation-en
Fetched 20.3 MB in 9s (2,215 kB/s)
Reading package lists... Done
lee@lee-linux:~$ sudo apt-get upgrade
Reading package lists... Done
Building dependency tree
Reading state information... Done
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
lee@lee-linux:~$

Perfect. No errors. Nothing to upgrade. Where is your problem?

The problem is that Lee is mixing repositories from different distributions of Linux (sarge and precise). Mixing incompatible repositories can and will break his package manager, as proven in the output above....

The Terminal output above shows the following issue:

lee@lee-linux:~$ sudo cp /var/lib/dpkg/status-old /var/lib/dpkg/status
cp: cannot stat `/var/lib/dpkg/status-old': No such file or directory

This is NOT normal. Ubuntu cannot find the file /var/lib/dpkg/status-old, even though it SHOULD have been there....

This leads me to believe the package manager is still broken....

Mark, thanks for the intervention.
I've acknowledged third party repos incl. sarge. When someone adds such repos I assume the person is aware of risks and has reasons since those steps are interactive. The result from #6 didn't lead me to worry about sarge or status-old.
Maybe Lee would be so kind to post the output of:
ls -al /var/lib/dpkg/

Hi Sam thanks for your response. Here is the output:

lee@lee-linux:~$ ls -al /var/lib/dpkg/
total 8
drwxr-xr-x 2 root root 4096 Jul 10 08:11 .
drwxr-xr-x 83 root root 4096 Jul 8 18:24 ..
-rw-r--r-- 1 root root 0 Jul 9 18:44 available
-rw-r--r-- 1 root root 0 Jul 9 18:11 available-bad
-rw-r--r-- 1 root root 0 Jul 9 18:42 available-old
-rw-r----- 1 root root 0 Jul 9 18:44 lock
-rw-r--r-- 1 root root 0 Jul 9 18:11 status

Output looks indeed a bit less.
Ok, the last days and today arrived some updates, please test if apt works, please don't open any GUIs except terminal, if there is a problem it's easier to deal with by cli. Thanks.
Please post output of:
sudo apt-get update
sudo apt-get upgrade

Attached - no updates!

lee@lee-linux:~$ sudo apt-get update
[sudo] password for lee:
Ign http://webmin.mirror.somersettechsolutions.co.uk sarge InRelease
Ign http://dl.google.com stable InRelease
Ign http://extras.ubuntu.com precise InRelease
Ign http://archive.ubuntu.com precise InRelease
Ign http://archive.ubuntu.com precise-updates InRelease
Ign http://archive.ubuntu.com precise-backports InRelease
Ign http://archive.ubuntu.com precise-security InRelease
Ign http://archive.ubuntu.com precise-proposed InRelease
Hit http://webmin.mirror.somersettechsolutions.co.uk sarge Release.gpg
Ign http://dl.google.com stable InRelease
Hit http://extras.ubuntu.com precise Release.gpg
Get:1 http://archive.ubuntu.com precise Release.gpg [198 B]
Hit http://webmin.mirror.somersettechsolutions.co.uk sarge Release
Get:2 http://dl.google.com stable Release.gpg [198 B]
Hit http://extras.ubuntu.com precise Release
Get:3 http://archive.ubuntu.com precise-updates Release.gpg [198 B]
Get:4 http://archive.ubuntu.com precise-backports Release.gpg [198 B]
Get:5 http://archive.ubuntu.com precise-security Release.gpg [198 B]
Get:6 http://dl.google.com stable Release.gpg [198 B]
Hit http://extras.ubuntu.com precise/main Sources
Get:7 http://archive.ubuntu.com precise-proposed Release.gpg [198 B]
Hit http://webmin.mirror.somersettechsolutions.co.uk sarge/contrib amd64 Packages
Get:8 http://archive.ubuntu.com precise Release [49.6 kB]
Hit http://extras.ubuntu.com precise/main amd64 Packages
Hit http://extras.ubuntu.com precise/main i386 Packages
Hit http://webmin.mirror.somersettechsolutions.co.uk sarge/contrib i386 Packages
Ign http://webmin.mirror.somersettechsolutions.co.uk sarge/contrib TranslationIndex
Ign http://extras.ubuntu.com precise/main TranslationIndex
Get:9 http://archive.ubuntu.com precise-updates Release [49.6 kB]
Get:10 http://archive.ubuntu.com precise-backports Release [49.6 kB]
Ign http://download.webmin.com sarge InRelease
Get:11 http://archive.ubuntu.com precise-security Release [49.6 kB]
Get:12 http://archive.ubuntu.com precise-proposed Release [49.6 kB]
Get:13 http://archive.ubuntu.com precise/main Sources [934 kB]
Ign http://software.virtualmin.com virtualmin-precise InRelease
Ign http://webmin.mirror.somersettechsolutions.co.uk sarge/contrib Translation-en_GB
Ign http://extras.ubuntu.com precise/main Translation-en_GB
Ign http://webmin.mirror.somersettechsolutions.co.uk sarge/contrib Translation-en
Ign http://extras.ubuntu.com precise/main Translation-en
Hit http://download.webmin.com sarge Release.gpg
Ign http://software.virtualmin.com virtualmin-universal InRelease
Get:14 http://archive.ubuntu.com precise/restricted Sources [5,470 B]
Get:15 http://archive.ubuntu.com precise/universe Sources [5,019 kB]
Hit http://software.virtualmin.com virtualmin-precise Release.gpg
Hit http://download.webmin.com sarge Release
Hit http://software.virtualmin.com virtualmin-universal Release.gpg
Hit http://download.webmin.com sarge/contrib amd64 Packages
Hit http://software.virtualmin.com virtualmin-precise Release
Hit http://download.webmin.com sarge/contrib i386 Packages
Hit http://software.virtualmin.com virtualmin-universal Release
Get:16 http://archive.ubuntu.com precise/multiverse Sources [155 kB]
Get:17 http://archive.ubuntu.com precise/main amd64 Packages [1,273 kB]
Get:18 http://archive.ubuntu.com precise/restricted amd64 Packages [8,452 B]
Get:19 http://archive.ubuntu.com precise/universe amd64 Packages [4,786 kB]
Hit http://software.virtualmin.com virtualmin-precise/main amd64 Packages
Ign http://download.webmin.com sarge/contrib TranslationIndex
Hit http://software.virtualmin.com virtualmin-precise/main i386 Packages
Get:20 http://archive.ubuntu.com precise/multiverse amd64 Packages [119 kB]
Get:21 http://archive.ubuntu.com precise/main i386 Packages [1,274 kB]
Ign http://software.virtualmin.com virtualmin-precise/main TranslationIndex
Get:22 http://archive.ubuntu.com precise/restricted i386 Packages [8,431 B]
Get:23 http://archive.ubuntu.com precise/universe i386 Packages [4,796 kB]
Get:24 http://dl.google.com stable Release [1,347 B]
Get:25 http://dl.google.com stable Release [1,338 B]
Get:26 http://dl.google.com stable/main amd64 Packages [1,249 B]
Hit http://software.virtualmin.com virtualmin-universal/main amd64 Packages
Get:27 http://dl.google.com stable/main i386 Packages [1,243 B]
Ign http://dl.google.com stable/main TranslationIndex
Get:28 http://dl.google.com stable/main amd64 Packages [469 B]
Get:29 http://dl.google.com stable/main i386 Packages [464 B]
Ign http://dl.google.com stable/main TranslationIndex
Hit http://software.virtualmin.com virtualmin-universal/main i386 Packages
Get:30 http://archive.ubuntu.com precise/multiverse i386 Packages [121 kB]
Hit http://archive.ubuntu.com precise/main TranslationIndex
Hit http://archive.ubuntu.com precise/multiverse TranslationIndex
Hit http://archive.ubuntu.com precise/restricted TranslationIndex
Hit http://archive.ubuntu.com precise/universe TranslationIndex
Get:31 http://archive.ubuntu.com precise-updates/main Sources [127 kB]
Get:32 http://archive.ubuntu.com precise-updates/restricted Sources [1,379 B]
Get:33 http://archive.ubuntu.com precise-updates/universe Sources [33.0 kB]
Get:34 http://archive.ubuntu.com precise-updates/multiverse Sources [1,058 B]
Get:35 http://archive.ubuntu.com precise-updates/main amd64 Packages [318 kB]
Get:36 http://archive.ubuntu.com precise-updates/restricted amd64 Packages [2,417 B]
Get:37 http://archive.ubuntu.com precise-updates/universe amd64 Packages [88.0 kB]
Get:38 http://archive.ubuntu.com precise-updates/multiverse amd64 Packages [1,829 B]
Get:39 http://archive.ubuntu.com precise-updates/main i386 Packages [321 kB]
Get:40 http://archive.ubuntu.com precise-updates/restricted i386 Packages [2,439 B]
Get:41 http://archive.ubuntu.com precise-updates/universe i386 Packages [88.6 kB]
Get:42 http://archive.ubuntu.com precise-updates/multiverse i386 Packages [2,047 B]
Hit http://archive.ubuntu.com precise-updates/main TranslationIndex
Hit http://archive.ubuntu.com precise-updates/multiverse TranslationIndex
Hit http://archive.ubuntu.com precise-updates/restricted TranslationIndex
Hit http://archive.ubuntu.com precise-updates/universe TranslationIndex
Get:43 http://archive.ubuntu.com precise-backports/main Sources [1,845 B]
Get:44 http://archive.ubuntu.com precise-backports/restricted Sources [14 B]
Get:45 http://archive.ubuntu.com precise-backports/universe Sources [11.9 kB]
Get:46 http://archive.ubuntu.com precise-backports/multiverse Sources [1,383 B]
Get:47 http://archive.ubuntu.com precise-backports/main amd64 Packages [1,271 B]
Get:48 http://archive.ubuntu.com precise-backports/restricted amd64 Packages [14 B]
Get:49 http://archive.ubuntu.com precise-backports/universe amd64 Packages [10.1 kB]
Get:50 http://archive.ubuntu.com precise-backports/multiverse amd64 Packages [996 B]
Get:51 http://archive.ubuntu.com precise-backports/main i386 Packages [1,271 B]
Get:52 http://archive.ubuntu.com precise-backports/restricted i386 Packages [14 B]
Get:53 http://archive.ubuntu.com precise-backports/universe i386 Packages [10.2 kB]
Get:54 http://archive.ubuntu.com precise-backports/multiverse i386 Packages [999 B]
Hit http://archive.ubuntu.com precise-backports/main TranslationIndex
Hit http://archive.ubuntu.com precise-backports/multiverse TranslationIndex
Hit http://archive.ubuntu.com precise-backports/restricted TranslationIndex
Hit http://archive.ubuntu.com precise-backports/universe TranslationIndex
Get:55 http://archive.ubuntu.com precise-security/main Sources [24.8 kB]
Ign http://dl.google.com stable/main Translation-en_GB
Ign http://dl.google.com stable/main Translation-en
Get:56 http://archive.ubuntu.com precise-security/restricted Sources [14 B]
Get:57 http://archive.ubuntu.com precise-security/universe Sources [7,832 B]
Get:58 http://archive.ubuntu.com precise-security/multiverse Sources [713 B]
Ign http://dl.google.com stable/main Translation-en_GB
Ign http://software.virtualmin.com virtualmin-universal/main TranslationIndex
Ign http://dl.google.com stable/main Translation-en
Get:59 http://archive.ubuntu.com precise-security/main amd64 Packages [73.0 kB]
Get:60 http://archive.ubuntu.com precise-security/restricted amd64 Packages [14 B]
Get:61 http://archive.ubuntu.com precise-security/universe amd64 Packages [19.5 kB]
Get:62 http://archive.ubuntu.com precise-security/multiverse amd64 Packages [1,155 B]
Get:63 http://archive.ubuntu.com precise-security/main i386 Packages [75.5 kB]
Get:64 http://archive.ubuntu.com precise-security/restricted i386 Packages [14 B]
Get:65 http://archive.ubuntu.com precise-security/universe i386 Packages [19.7 kB]
Get:66 http://archive.ubuntu.com precise-security/multiverse i386 Packages [1,394 B]
Hit http://archive.ubuntu.com precise-security/main TranslationIndex
Hit http://archive.ubuntu.com precise-security/multiverse TranslationIndex
Hit http://archive.ubuntu.com precise-security/restricted TranslationIndex
Hit http://archive.ubuntu.com precise-security/universe TranslationIndex
Get:67 http://archive.ubuntu.com precise-proposed/restricted amd64 Packages [14 B]
Get:68 http://archive.ubuntu.com precise-proposed/main amd64 Packages [160 kB]
Get:69 http://archive.ubuntu.com precise-proposed/multiverse amd64 Packages [14 B]
Get:70 http://archive.ubuntu.com precise-proposed/universe amd64 Packages [19.4 kB]
Get:71 http://archive.ubuntu.com precise-proposed/restricted i386 Packages [14 B]
Get:72 http://archive.ubuntu.com precise-proposed/main i386 Packages [162 kB]
Get:73 http://archive.ubuntu.com precise-proposed/multiverse i386 Packages [14 B]
Get:74 http://archive.ubuntu.com precise-proposed/universe i386 Packages [19.3 kB]
Get:75 http://archive.ubuntu.com precise-proposed/main TranslationIndex [3,564 B]
Get:76 http://archive.ubuntu.com precise-proposed/multiverse TranslationIndex [2,605 B]
Get:77 http://archive.ubuntu.com precise-proposed/restricted TranslationIndex [2,461 B]
Get:78 http://archive.ubuntu.com precise-proposed/universe TranslationIndex [2,850 B]
Hit http://archive.ubuntu.com precise/main Translation-en_GB
Hit http://archive.ubuntu.com precise/main Translation-en
Hit http://archive.ubuntu.com precise/multiverse Translation-en_GB
Hit http://archive.ubuntu.com precise/multiverse Translation-en
Hit http://archive.ubuntu.com precise/restricted Translation-en_GB
Hit http://archive.ubuntu.com precise/restricted Translation-en
Hit http://archive.ubuntu.com precise/universe Translation-en_GB
Hit http://archive.ubuntu.com precise/universe Translation-en
Hit http://archive.ubuntu.com precise-updates/main Translation-en
Hit http://archive.ubuntu.com precise-updates/multiverse Translation-en
Hit http://archive.ubuntu.com precise-updates/restricted Translation-en
Hit http://archive.ubuntu.com precise-updates/universe Translation-en
Hit http://archive.ubuntu.com precise-backports/main Translation-en
Hit http://archive.ubuntu.com precise-backports/multiverse Translation-en
Hit http://archive.ubuntu.com precise-backports/restricted Translation-en
Hit http://archive.ubuntu.com precise-backports/universe Translation-en
Hit http://archive.ubuntu.com precise-security/main Translation-en
Hit http://archive.ubuntu.com precise-security/multiverse Translation-en
Hit http://archive.ubuntu.com precise-security/restricted Translation-en
Hit http://archive.ubuntu.com precise-security/universe Translation-en
Hit http://archive.ubuntu.com precise-proposed/main Translation-en_GB
Get:79 http://archive.ubuntu.com precise-proposed/main Translation-en [52.7 kB]
Hit http://archive.ubuntu.com precise-proposed/multiverse Translation-en_GB
Hit http://archive.ubuntu.com precise-proposed/multiverse Translation-en
Hit http://archive.ubuntu.com precise-proposed/restricted Translation-en_GB
Hit http://archive.ubuntu.com precise-proposed/restricted Translation-en
Hit http://archive.ubuntu.com precise-proposed/universe Translation-en_GB
Hit http://archive.ubuntu.com precise-proposed/universe Translation-en
Ign http://download.webmin.com sarge/contrib Translation-en_GB
Ign http://download.webmin.com sarge/contrib Translation-en
Ign http://software.virtualmin.com virtualmin-precise/main Translation-en_GB
Ign http://software.virtualmin.com virtualmin-precise/main Translation-en
Ign http://software.virtualmin.com virtualmin-universal/main Translation-en_GB
Ign http://software.virtualmin.com virtualmin-universal/main Translation-en
Fetched 20.4 MB in 10s (1,962 kB/s)
Reading package lists... Done
lee@lee-linux:~$ sudo apt-get upgrade
Reading package lists... Done
Building dependency tree
Reading state information... Done
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
lee@lee-linux:~$

Yes, I am still having the problem - no updates

Please disable third party sources and test update again.
https://help.ubuntu.com/community/Repositories/Ubuntu#Third-Party_Software_Tab

Ok all disabled - still does not update:

lee@lee-linux:~$ sudo apt-get update
[sudo] password for lee:
Ign http://archive.ubuntu.com precise InRelease
Ign http://archive.ubuntu.com precise-updates InRelease
Ign http://archive.ubuntu.com precise-backports InRelease
Ign http://archive.ubuntu.com precise-security InRelease
Ign http://archive.ubuntu.com precise-proposed InRelease
Get:1 http://archive.ubuntu.com precise Release.gpg [198 B]
Get:2 http://archive.ubuntu.com precise-updates Release.gpg [198 B]
Get:3 http://archive.ubuntu.com precise-backports Release.gpg [198 B]
Get:4 http://archive.ubuntu.com precise-security Release.gpg [198 B]
Get:5 http://archive.ubuntu.com precise-proposed Release.gpg [198 B]
Get:6 http://archive.ubuntu.com precise Release [49.6 kB]
Get:7 http://archive.ubuntu.com precise-updates Release [49.6 kB]
Get:8 http://archive.ubuntu.com precise-backports Release [49.6 kB]
Get:9 http://archive.ubuntu.com precise-security Release [49.6 kB]
Get:10 http://archive.ubuntu.com precise-proposed Release [49.6 kB]
Get:11 http://archive.ubuntu.com precise/main Sources [934 kB]
Get:12 http://archive.ubuntu.com precise/restricted Sources [5,470 B]
Get:13 http://archive.ubuntu.com precise/universe Sources [5,019 kB]
Get:14 http://archive.ubuntu.com precise/multiverse Sources [155 kB]
Get:15 http://archive.ubuntu.com precise/main amd64 Packages [1,273 kB]
Get:16 http://archive.ubuntu.com precise/restricted amd64 Packages [8,452 B]
Get:17 http://archive.ubuntu.com precise/universe amd64 Packages [4,786 kB]
Get:18 http://archive.ubuntu.com precise/multiverse amd64 Packages [119 kB]
Get:19 http://archive.ubuntu.com precise/main i386 Packages [1,274 kB]
Get:20 http://archive.ubuntu.com precise/restricted i386 Packages [8,431 B]
Get:21 http://archive.ubuntu.com precise/universe i386 Packages [4,796 kB]
Get:22 http://archive.ubuntu.com precise/multiverse i386 Packages [121 kB]
Hit http://archive.ubuntu.com precise/main TranslationIndex
Hit http://archive.ubuntu.com precise/multiverse TranslationIndex
Hit http://archive.ubuntu.com precise/restricted TranslationIndex
Hit http://archive.ubuntu.com precise/universe TranslationIndex
Get:23 http://archive.ubuntu.com precise-updates/main Sources [128 kB]
Get:24 http://archive.ubuntu.com precise-updates/restricted Sources [1,379 B]
Get:25 http://archive.ubuntu.com precise-updates/universe Sources [33.0 kB]
Get:26 http://archive.ubuntu.com precise-updates/multiverse Sources [1,058 B]
Get:27 http://archive.ubuntu.com precise-updates/main amd64 Packages [319 kB]
Get:28 http://archive.ubuntu.com precise-updates/restricted amd64 Packages [2,417 B]
Get:29 http://archive.ubuntu.com precise-updates/universe amd64 Packages [88.8 kB]
Get:30 http://archive.ubuntu.com precise-updates/multiverse amd64 Packages [1,829 B]
Get:31 http://archive.ubuntu.com precise-updates/main i386 Packages [321 kB]
Get:32 http://archive.ubuntu.com precise-updates/restricted i386 Packages [2,439 B]
Get:33 http://archive.ubuntu.com precise-updates/universe i386 Packages [89.3 kB]
Get:34 http://archive.ubuntu.com precise-updates/multiverse i386 Packages [2,047 B]
Hit http://archive.ubuntu.com precise-updates/main TranslationIndex
Hit http://archive.ubuntu.com precise-updates/multiverse TranslationIndex
Hit http://archive.ubuntu.com precise-updates/restricted TranslationIndex
Hit http://archive.ubuntu.com precise-updates/universe TranslationIndex
Get:35 http://archive.ubuntu.com precise-backports/main Sources [1,845 B]
Get:36 http://archive.ubuntu.com precise-backports/restricted Sources [14 B]
Get:37 http://archive.ubuntu.com precise-backports/universe Sources [11.9 kB]
Get:38 http://archive.ubuntu.com precise-backports/multiverse Sources [1,383 B]
Get:39 http://archive.ubuntu.com precise-backports/main amd64 Packages [1,271 B]
Get:40 http://archive.ubuntu.com precise-backports/restricted amd64 Packages [14 B]
Get:41 http://archive.ubuntu.com precise-backports/universe amd64 Packages [10.1 kB]
Get:42 http://archive.ubuntu.com precise-backports/multiverse amd64 Packages [996 B]
Get:43 http://archive.ubuntu.com precise-backports/main i386 Packages [1,271 B]
Get:44 http://archive.ubuntu.com precise-backports/restricted i386 Packages [14 B]
Get:45 http://archive.ubuntu.com precise-backports/universe i386 Packages [10.2 kB]
Get:46 http://archive.ubuntu.com precise-backports/multiverse i386 Packages [999 B]
Hit http://archive.ubuntu.com precise-backports/main TranslationIndex
Hit http://archive.ubuntu.com precise-backports/multiverse TranslationIndex
Hit http://archive.ubuntu.com precise-backports/restricted TranslationIndex
Hit http://archive.ubuntu.com precise-backports/universe TranslationIndex
Get:47 http://archive.ubuntu.com precise-security/main Sources [26.1 kB]
Get:48 http://archive.ubuntu.com precise-security/restricted Sources [14 B]
Get:49 http://archive.ubuntu.com precise-security/universe Sources [7,832 B]
Get:50 http://archive.ubuntu.com precise-security/multiverse Sources [713 B]
Get:51 http://archive.ubuntu.com precise-security/main amd64 Packages [75.8 kB]
Get:52 http://archive.ubuntu.com precise-security/restricted amd64 Packages [14 B]
Get:53 http://archive.ubuntu.com precise-security/universe amd64 Packages [20.5 kB]
Get:54 http://archive.ubuntu.com precise-security/multiverse amd64 Packages [1,155 B]
Get:55 http://archive.ubuntu.com precise-security/main i386 Packages [78.4 kB]
Get:56 http://archive.ubuntu.com precise-security/restricted i386 Packages [14 B]
Get:57 http://archive.ubuntu.com precise-security/universe i386 Packages [20.7 kB]
Get:58 http://archive.ubuntu.com precise-security/multiverse i386 Packages [1,394 B]
Hit http://archive.ubuntu.com precise-security/main TranslationIndex
Hit http://archive.ubuntu.com precise-security/multiverse TranslationIndex
Hit http://archive.ubuntu.com precise-security/restricted TranslationIndex
Hit http://archive.ubuntu.com precise-security/universe TranslationIndex
Get:59 http://archive.ubuntu.com precise-proposed/restricted amd64 Packages [14 B]
Get:60 http://archive.ubuntu.com precise-proposed/main amd64 Packages [163 kB]
Get:61 http://archive.ubuntu.com precise-proposed/multiverse amd64 Packages [14 B]
Get:62 http://archive.ubuntu.com precise-proposed/universe amd64 Packages [22.5 kB]
Get:63 http://archive.ubuntu.com precise-proposed/restricted i386 Packages [14 B]
Get:64 http://archive.ubuntu.com precise-proposed/main i386 Packages [164 kB]
Get:65 http://archive.ubuntu.com precise-proposed/multiverse i386 Packages [14 B]
Get:66 http://archive.ubuntu.com precise-proposed/universe i386 Packages [22.5 kB]
Hit http://archive.ubuntu.com precise-proposed/main TranslationIndex
Hit http://archive.ubuntu.com precise-proposed/multiverse TranslationIndex
Hit http://archive.ubuntu.com precise-proposed/restricted TranslationIndex
Hit http://archive.ubuntu.com precise-proposed/universe TranslationIndex
Get:67 http://archive.ubuntu.com precise/main Translation-en_GB [96.4 kB]
Hit http://archive.ubuntu.com precise/main Translation-en
Get:68 http://archive.ubuntu.com precise/multiverse Translation-en_GB [79.8 kB]
Hit http://archive.ubuntu.com precise/multiverse Translation-en
Get:69 http://archive.ubuntu.com precise/restricted Translation-en_GB [2,406 B]
Hit http://archive.ubuntu.com precise/restricted Translation-en
Get:70 http://archive.ubuntu.com precise/universe Translation-en_GB [5,492 B]
Hit http://archive.ubuntu.com precise/universe Translation-en
Hit http://archive.ubuntu.com precise-updates/main Translation-en
Hit http://archive.ubuntu.com precise-updates/multiverse Translation-en
Hit http://archive.ubuntu.com precise-updates/restricted Translation-en
Hit http://archive.ubuntu.com precise-updates/universe Translation-en
Hit http://archive.ubuntu.com precise-backports/main Translation-en
Hit http://archive.ubuntu.com precise-backports/multiverse Translation-en
Hit http://archive.ubuntu.com precise-backports/restricted Translation-en
Hit http://archive.ubuntu.com precise-backports/universe Translation-en
Hit http://archive.ubuntu.com precise-security/main Translation-en
Hit http://archive.ubuntu.com precise-security/multiverse Translation-en
Hit http://archive.ubuntu.com precise-security/restricted Translation-en
Hit http://archive.ubuntu.com precise-security/universe Translation-en
Get:71 http://archive.ubuntu.com precise-proposed/main Translation-en_GB [96.4 kB]
Hit http://archive.ubuntu.com precise-proposed/main Translation-en
Get:72 http://archive.ubuntu.com precise-proposed/multiverse Translation-en_GB [79.8 kB]
Hit http://archive.ubuntu.com precise-proposed/multiverse Translation-en
Get:73 http://archive.ubuntu.com precise-proposed/restricted Translation-en_GB [2,406 B]
Hit http://archive.ubuntu.com precise-proposed/restricted Translation-en
Get:74 http://archive.ubuntu.com precise-proposed/universe Translation-en_GB [5,492 B]
Hit http://archive.ubuntu.com precise-proposed/universe Translation-en
Fetched 20.8 MB in 10s (1,925 kB/s)
Reading package lists... Done
lee@lee-linux:~$ sudo apt-get upgrade
Reading package lists... Done
Building dependency tree
Reading state information... Done
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
lee@lee-linux:~$

I think that the only remaining issue here is this Terminal output:

lee@lee-linux:~$ ls -al /var/lib/dpkg/
total 8
drwxr-xr-x 2 root root 4096 Jul 10 08:11 .
drwxr-xr-x 83 root root 4096 Jul 8 18:24 ..
-rw-r--r-- 1 root root 0 Jul 9 18:44 available
-rw-r--r-- 1 root root 0 Jul 9 18:11 available-bad
-rw-r--r-- 1 root root 0 Jul 9 18:42 available-old
-rw-r----- 1 root root 0 Jul 9 18:44 lock
-rw-r--r-- 1 root root 0 Jul 9 18:11 status

So your /var/lib/dpkg/status file AND your /var/lib/dpkg/available file are empty (size: 0 bytes), but they should normally NOT be empty.
To me: an empty status file and empty available file is a CORRUPT file.

You will need to restore from backup by running the following Terminal commands:

sudo mv /var/lib/dpkg/available /var/lib/dpkg/available.oldBusted
sudo touch /var/lib/dpkg/available
sudo cp /var/backups/dpkg.status.1.gz /var/lib/dpkg/
sudo gunzip -d /var/lib/dpkg/dpkg.status.1.gz
sudo mv /var/lib/dpkg/dpkg.status.1 /var/lib/dpkg/status
sudo dpkg --clear-avail

Then retest updating.

Mark - unfortunately this has not helped - see output below:

lee@lee-linux:~$ sudo mv /var/lib/dpkg/available /var/lib/dpkg/available.oldBusted
[sudo] password for lee:
lee@lee-linux:~$ sudo touch /var/lib/dpkg/available
lee@lee-linux:~$ sudo cp /var/backups/dpkg.status.1.gz /var/lib/dpkg/
lee@lee-linux:~$ sudo gunzip -d /var/lib/dpkg/dpkg.status.1.gz
lee@lee-linux:~$ sudo mv /var/lib/dpkg/dpkg.status.1 /var/lib/dpkg/status
lee@lee-linux:~$ sudo dpkg --clear-avail
lee@lee-linux:~$ sudo apt-get update
Ign http://archive.ubuntu.com precise InRelease
Ign http://archive.ubuntu.com precise-updates InRelease
Ign http://archive.ubuntu.com precise-backports InRelease
Ign http://archive.ubuntu.com precise-security InRelease
Ign http://archive.ubuntu.com precise-proposed InRelease
Get:1 http://archive.ubuntu.com precise Release.gpg [198 B]
Get:2 http://archive.ubuntu.com precise-updates Release.gpg [198 B]
Get:3 http://archive.ubuntu.com precise-backports Release.gpg [198 B]
Get:4 http://archive.ubuntu.com precise-security Release.gpg [198 B]
Get:5 http://archive.ubuntu.com precise-proposed Release.gpg [198 B]
Get:6 http://archive.ubuntu.com precise Release [49.6 kB]
Get:7 http://archive.ubuntu.com precise-updates Release [49.6 kB]
Get:8 http://archive.ubuntu.com precise-backports Release [49.6 kB]
Get:9 http://archive.ubuntu.com precise-security Release [49.6 kB]
Get:10 http://archive.ubuntu.com precise-proposed Release [49.6 kB]
Get:11 http://archive.ubuntu.com precise/main Sources [934 kB]
Get:12 http://archive.ubuntu.com precise/restricted Sources [5,470 B]
Get:13 http://archive.ubuntu.com precise/universe Sources [5,019 kB]
Get:14 http://archive.ubuntu.com precise/multiverse Sources [155 kB]
Get:15 http://archive.ubuntu.com precise/main amd64 Packages [1,273 kB]
Get:16 http://archive.ubuntu.com precise/restricted amd64 Packages [8,452 B]
Get:17 http://archive.ubuntu.com precise/universe amd64 Packages [4,786 kB]
Get:18 http://archive.ubuntu.com precise/multiverse amd64 Packages [119 kB]
Get:19 http://archive.ubuntu.com precise/main i386 Packages [1,274 kB]
Get:20 http://archive.ubuntu.com precise/restricted i386 Packages [8,431 B]
Get:21 http://archive.ubuntu.com precise/universe i386 Packages [4,796 kB]
Get:22 http://archive.ubuntu.com precise/multiverse i386 Packages [121 kB]
Hit http://archive.ubuntu.com precise/main TranslationIndex
Hit http://archive.ubuntu.com precise/multiverse TranslationIndex
Hit http://archive.ubuntu.com precise/restricted TranslationIndex
Hit http://archive.ubuntu.com precise/universe TranslationIndex
Get:23 http://archive.ubuntu.com precise-updates/main Sources [128 kB]
Get:24 http://archive.ubuntu.com precise-updates/restricted Sources [1,379 B]
Get:25 http://archive.ubuntu.com precise-updates/universe Sources [33.0 kB]
Get:26 http://archive.ubuntu.com precise-updates/multiverse Sources [1,058 B]
Get:27 http://archive.ubuntu.com precise-updates/main amd64 Packages [319 kB]
Get:28 http://archive.ubuntu.com precise-updates/restricted amd64 Packages [2,417 B]
Get:29 http://archive.ubuntu.com precise-updates/universe amd64 Packages [88.8 kB]
Get:30 http://archive.ubuntu.com precise-updates/multiverse amd64 Packages [1,829 B]
Get:31 http://archive.ubuntu.com precise-updates/main i386 Packages [321 kB]
Get:32 http://archive.ubuntu.com precise-updates/restricted i386 Packages [2,439 B]
Get:33 http://archive.ubuntu.com precise-updates/universe i386 Packages [89.3 kB]
Get:34 http://archive.ubuntu.com precise-updates/multiverse i386 Packages [2,047 B]
Hit http://archive.ubuntu.com precise-updates/main TranslationIndex
Hit http://archive.ubuntu.com precise-updates/multiverse TranslationIndex
Hit http://archive.ubuntu.com precise-updates/restricted TranslationIndex
Hit http://archive.ubuntu.com precise-updates/universe TranslationIndex
Get:35 http://archive.ubuntu.com precise-backports/main Sources [1,845 B]
Get:36 http://archive.ubuntu.com precise-backports/restricted Sources [14 B]
Get:37 http://archive.ubuntu.com precise-backports/universe Sources [11.9 kB]
Get:38 http://archive.ubuntu.com precise-backports/multiverse Sources [1,383 B]
Get:39 http://archive.ubuntu.com precise-backports/main amd64 Packages [1,271 B]
Get:40 http://archive.ubuntu.com precise-backports/restricted amd64 Packages [14 B]
Get:41 http://archive.ubuntu.com precise-backports/universe amd64 Packages [10.1 kB]
Get:42 http://archive.ubuntu.com precise-backports/multiverse amd64 Packages [996 B]
Get:43 http://archive.ubuntu.com precise-backports/main i386 Packages [1,271 B]
Get:44 http://archive.ubuntu.com precise-backports/restricted i386 Packages [14 B]
Get:45 http://archive.ubuntu.com precise-backports/universe i386 Packages [10.2 kB]
Get:46 http://archive.ubuntu.com precise-backports/multiverse i386 Packages [999 B]
Hit http://archive.ubuntu.com precise-backports/main TranslationIndex
Hit http://archive.ubuntu.com precise-backports/multiverse TranslationIndex
Hit http://archive.ubuntu.com precise-backports/restricted TranslationIndex
Hit http://archive.ubuntu.com precise-backports/universe TranslationIndex
Get:47 http://archive.ubuntu.com precise-security/main Sources [26.1 kB]
Get:48 http://archive.ubuntu.com precise-security/restricted Sources [14 B]
Get:49 http://archive.ubuntu.com precise-security/universe Sources [7,832 B]
Get:50 http://archive.ubuntu.com precise-security/multiverse Sources [713 B]
Get:51 http://archive.ubuntu.com precise-security/main amd64 Packages [75.8 kB]
Get:52 http://archive.ubuntu.com precise-security/restricted amd64 Packages [14 B]
Get:53 http://archive.ubuntu.com precise-security/universe amd64 Packages [20.5 kB]
Get:54 http://archive.ubuntu.com precise-security/multiverse amd64 Packages [1,155 B]
Get:55 http://archive.ubuntu.com precise-security/main i386 Packages [78.4 kB]
Get:56 http://archive.ubuntu.com precise-security/restricted i386 Packages [14 B]
Get:57 http://archive.ubuntu.com precise-security/universe i386 Packages [20.7 kB]
Get:58 http://archive.ubuntu.com precise-security/multiverse i386 Packages [1,394 B]
Hit http://archive.ubuntu.com precise-security/main TranslationIndex
Hit http://archive.ubuntu.com precise-security/multiverse TranslationIndex
Hit http://archive.ubuntu.com precise-security/restricted TranslationIndex
Hit http://archive.ubuntu.com precise-security/universe TranslationIndex
Get:59 http://archive.ubuntu.com precise-proposed/restricted amd64 Packages [14 B]
Get:60 http://archive.ubuntu.com precise-proposed/main amd64 Packages [163 kB]
Get:61 http://archive.ubuntu.com precise-proposed/multiverse amd64 Packages [14 B]
Get:62 http://archive.ubuntu.com precise-proposed/universe amd64 Packages [22.5 kB]
Get:63 http://archive.ubuntu.com precise-proposed/restricted i386 Packages [14 B]
Get:64 http://archive.ubuntu.com precise-proposed/main i386 Packages [164 kB]
Get:65 http://archive.ubuntu.com precise-proposed/multiverse i386 Packages [14 B]
Get:66 http://archive.ubuntu.com precise-proposed/universe i386 Packages [22.5 kB]
Hit http://archive.ubuntu.com precise-proposed/main TranslationIndex
Hit http://archive.ubuntu.com precise-proposed/multiverse TranslationIndex
Hit http://archive.ubuntu.com precise-proposed/restricted TranslationIndex
Hit http://archive.ubuntu.com precise-proposed/universe TranslationIndex
Hit http://archive.ubuntu.com precise/main Translation-en_GB
Hit http://archive.ubuntu.com precise/main Translation-en
Hit http://archive.ubuntu.com precise/multiverse Translation-en_GB
Hit http://archive.ubuntu.com precise/multiverse Translation-en
Hit http://archive.ubuntu.com precise/restricted Translation-en_GB
Hit http://archive.ubuntu.com precise/restricted Translation-en
Hit http://archive.ubuntu.com precise/universe Translation-en_GB
Hit http://archive.ubuntu.com precise/universe Translation-en
Hit http://archive.ubuntu.com precise-updates/main Translation-en
Hit http://archive.ubuntu.com precise-updates/multiverse Translation-en
Hit http://archive.ubuntu.com precise-updates/restricted Translation-en
Hit http://archive.ubuntu.com precise-updates/universe Translation-en
Hit http://archive.ubuntu.com precise-backports/main Translation-en
Hit http://archive.ubuntu.com precise-backports/multiverse Translation-en
Hit http://archive.ubuntu.com precise-backports/restricted Translation-en
Hit http://archive.ubuntu.com precise-backports/universe Translation-en
Hit http://archive.ubuntu.com precise-security/main Translation-en
Hit http://archive.ubuntu.com precise-security/multiverse Translation-en
Hit http://archive.ubuntu.com precise-security/restricted Translation-en
Hit http://archive.ubuntu.com precise-security/universe Translation-en
Hit http://archive.ubuntu.com precise-proposed/main Translation-en_GB
Hit http://archive.ubuntu.com precise-proposed/main Translation-en
Hit http://archive.ubuntu.com precise-proposed/multiverse Translation-en_GB
Hit http://archive.ubuntu.com precise-proposed/multiverse Translation-en
Hit http://archive.ubuntu.com precise-proposed/restricted Translation-en_GB
Hit http://archive.ubuntu.com precise-proposed/restricted Translation-en
Hit http://archive.ubuntu.com precise-proposed/universe Translation-en_GB
Hit http://archive.ubuntu.com precise-proposed/universe Translation-en
Fetched 20.4 MB in 10s (1,886 kB/s)
Reading package lists... Done
lee@lee-linux:~$ sudo apt-get upgrade
Reading package lists... Done
Building dependency tree
Reading state information... Done
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
lee@lee-linux:~$

From the very first output
lee@lee-linux:~$ sudo mv /var/lib/dpkg/status /var/lib/dpkg/status-bad
lee@lee-linux:~$ sudo cp /var/lib/dpkg/status-old /var/lib/dpkg/status
cp: cannot stat `/var/lib/dpkg/status-old': No such file or directory

just wondering where the file status-bad is?
Please try:
sudo updatedb
locate status-bad

Anyway, there should be also a dpkg.status.0 in /var/backups is it also empty?

Sam: you're going in circles now. :-p

In your first post here, you asked Lee to run this:

sudo mv /var/lib/dpkg/status-bad /var/lib/dpkg/status

That explains where status-bad went.....

Hi Sam - here is the info requested:

lee@lee-linux:~$ sudo updatedb
[sudo] password for lee:
lee@lee-linux:~$ locate status-bad
/var/lib/dpkg.backup/dpkg/status-bad
lee@lee-linux:~$ cd /var/backups
lee@lee-linux:/var/backups$ ls -al /var/backups
total 3092
drwxr-xr-x 2 root root 4096 Jul 10 07:35 .
drwxr-xr-x 16 root root 4096 Jul 8 18:26 ..
-rw-r--r-- 1 root root 53729 Jul 8 17:59 apt.extended_states.0
-rw-r--r-- 1 root root 4483 Jul 1 11:33 apt.extended_states.1.gz
-rw-r--r-- 1 root root 4481 Jun 30 18:44 apt.extended_states.2.gz
-rw-r--r-- 1 root root 4249 Jun 30 00:13 apt.extended_states.3.gz
-rw-r--r-- 1 root root 4239 Jun 20 22:34 apt.extended_states.4.gz
-rw-r--r-- 1 root root 4220 Jun 18 19:22 apt.extended_states.5.gz
-rw-r--r-- 1 root root 4216 Jun 17 20:10 apt.extended_states.6.gz
-rw-r--r-- 1 root root 0 Jul 10 07:35 dpkg.status.0
-rw-r--r-- 1 root root 34 Jul 8 18:29 dpkg.status.1.gz
-rw-r--r-- 1 root root 580619 Jul 5 16:48 dpkg.status.2.gz
-rw-r--r-- 1 root root 580613 Jul 4 18:14 dpkg.status.3.gz
-rw-r--r-- 1 root root 580606 Jul 3 19:06 dpkg.status.4.gz
-rw-r--r-- 1 root root 580584 Jul 2 19:16 dpkg.status.5.gz
-rw-r--r-- 1 root root 580584 Jul 1 11:33 dpkg.status.6.gz
-rw------- 1 root root 1096 Jun 20 22:32 group.bak
-rw------- 1 root shadow 904 Jun 20 22:32 gshadow.bak
-rw------- 1 root root 2545 Jun 20 22:32 passwd.bak
-rw-r--r-- 1 root smmsp 64503 Jun 4 14:04 sendmail.cf.bak
-rw-r--r-- 1 root smmsp 4220 Jun 4 14:04 sendmail.mc.bak
-rw------- 1 root shadow 1579 Jun 20 22:32 shadow.bak
-rw-r--r-- 1 root smmsp 44038 Jun 4 14:04 submit.cf.bak
-rw-r--r-- 1 root smmsp 2381 Jun 4 14:04 submit.mc.bak

Mark, huh, thanks for the reminder.
That means status was already empty when moved to status-bad.
-rw-r--r-- 1 root root 0 Jul 10 07:35 dpkg.status.0

Ah, what's that, presumable empty.
lee@lee-linux:~$ locate status-bad
/var/lib/dpkg.backup/dpkg/status-bad

## I don't even have such a directory.

Lee, please post output of:
ls -al /var/lib/dpkg.backup/dpkg/status-bad

Hi Sam, as requested:

lee@lee-linux:~$ ls -al /var/lib/dpkg.backup/dpkg/status-bad
-rw-r--r-- 1 root root 0 Jul 8 18:29 /var/lib/dpkg.backup/dpkg/status-bad
lee@lee-linux:~$

Lee, apt doesn't update because it has no info what to update. In the output of #10
ls -al /var/lib/dpkg/
among others the 'info' directory is missing which contents all the prerm, postrm, preinst, postinst and other files.
How can directories like 'info', 'triggers', 'alternatives' disappear?
Are there somewhere else?
ls -al /var/lib/dpkg.backup/dpkg
or
ls -al /var/lib/dpkg.backup

as follows:

lee@lee-linux:~$ ls -al /var/lib/dpkg.backup/dpkg
total 8
drwxr-xr-x 2 root root 4096 Jul 9 18:03 .
drwxr-xr-x 3 root root 4096 Jul 9 16:45 ..
-rw-r--r-- 1 root root 0 Jul 9 18:11 available
-rw-r--r-- 1 root root 0 Jul 9 16:46 available-bad
-rw-r--r-- 1 root root 0 Jul 9 17:48 available-old
-rw-r----- 1 root root 0 Jul 9 18:32 lock
-rw-r--r-- 1 root root 0 Jul 9 18:11 status
-rw-r--r-- 1 root root 0 Jul 8 18:29 status-bad
lee@lee-linux:~$ ls -al /var/lib/dpkg.backup
total 12
drwxr-xr-x 3 root root 4096 Jul 9 16:45 .
drwxr-xr-x 83 root root 4096 Jul 8 18:24 ..
-rw-r--r-- 1 root root 0 Jul 8 18:09 available
drwxr-xr-x 2 root root 4096 Jul 9 18:03 dpkg
-rw-r----- 1 root root 0 Jul 8 18:23 lock

Thank you.
Please update database and locate some files supposed to be in 'info' directory.
sudo updatedb
locate apparmor.postrm
locate apt.preinst
locate apturl.postinst

lee@lee-linux:~$ sudo updatedb
[sudo] password for lee:
lee@lee-linux:~$ locate apparmor.postrm
lee@lee-linux:~$ locate apt.preinst
lee@lee-linux:~$ locate apturl.postinst
lee@lee-linux:~$

Thank you.
There're pretty much essentials in package management missing.
If you don't have those system files as backup somewhere I'd suggest to backup important personal data and reinstall from scratch.

Thanks Sam

Is there anyway to perform a "repair" install and keep Software like Webmin and virtualmin intact?
i.e. to overwrite my existing install woth a fresh install without having to re-format the drive?

Thanks
Lee

The installation from scratch doesn't include third party repos, otherwise it corrupts the system again, unless you remember what exactly causes the loss of essential files and the creation of obscure folders.
When there is a separate /home partition you only need to reinstall /.