deja dup cannot open files, nor can I

.gvfs is not a folder per se, i suggest you remove it from the scope

Have removed .gvfs from the scope of the backup.
What do you suggest for .cache/dconf?

All files in the .cache directory should be just used for temporarily caching some contents. If you delete one of them it should be automatically recreated in the moment they are needed.

I recommend you try the following terminal commands:

ls -la /home/john/.cache/dconf # to see file size, ownership and protection and
sudo fuser -v /home/john/.cache/dconf # to see who is accessing the file

Thank you for your help.
Nothing much happens when I ran the commands as you suggested
Here is the output:
john@john-p7-1109:~$ ls -la /home/john/.cache/dconf
ls: cannot open directory /home/john/.cache/dconf: Permission denied
john@john-p7-1109:~$ ls -la /home/john/.cache/dconf #
ls: cannot open directory /home/john/.cache/dconf: Permission denied
john@john-p7-1109:~$ sudo fuser -v /home/john/.cache/dconf #
[sudo] password for john:
Sorry, try again.
[sudo] password for john:
john@john-p7-1109:~$ sudo fuser -v /home/john/.cache/dconf #
john@john-p7-1109:~$ sudo fuser -v /home/john/.cache/dconf
john@john-p7-1109:~$

Perhaps what I should do is remove .cache from the scope of my backups
John

It seems that the protection on the .cache directory itself is wrong

What is the output of

ls -la /home/john/.c*
sudo ls -la /home/john/.cache/

Here is the output:
john@john-p7-1109:~$ ls -la /home/john/.c*
/home/john/.cache:
total 188
drwx------ 36 john john 4096 Mar 12 09:24 .
drwxr-xr-x 121 john john 12288 Apr 12 07:39 ..
drwxrwxr-x 3 john john 4096 Jul 28 2013 banshee-1
drwx------ 3 john john 4096 Aug 14 2013 chromium
drwx------ 2 john john 4096 Apr 3 08:22 compizconfig-1
drwx------ 2 root root 4096 Mar 12 12:09 dconf
drwxrwxr-x 3 john john 4096 Apr 10 03:17 deja-dup
-rw-r--r-- 1 john john 16384 Apr 2 07:32 event-sound-cache.tdb.436c9acdabeec30cab24765c51f2a1ee.i686-pc-linux-gnu
drwx------ 9 john john 4096 Oct 22 14:03 evolution
drwx------ 3 john john 4096 Oct 27 13:04 folks
drwxr-xr-x 2 john john 4096 Jan 10 16:17 fontconfig
drwx------ 3 john john 4096 Aug 1 2013 gegl-0.2
drwx------ 2 john john 4096 Oct 28 13:18 gnome-screenshot
drwxrwxr-x 2 john john 4096 Apr 13 08:04 gstreamer-1.0
drwxr-xr-x 3 john john 4096 Oct 18 14:24 ibus
drwx------ 3 john john 4096 Jul 26 2013 indicator
drwx------ 2 john john 4096 Jul 26 2013 indicator-appmenu
drwxr-xr-x 2 john john 4096 Oct 18 14:25 logrotate
drwxrwxr-x 4 john john 4096 Jan 11 15:52 media-art
drwx------ 3 john john 4096 Jul 26 2013 mozilla
drwxrwxr-x 3 john john 4096 Jul 26 2013 oneconf
drwx------ 3 john john 4096 Jul 28 2013 rhythmbox
drwxrwxr-x 3 john john 4096 Jul 31 2013 shotwell
drwxr-xr-x 3 john john 4096 Oct 25 18:52 signon-ui
drwx------ 3 john john 4096 Oct 20 08:26 simple-scan
drwxrwxr-x 8 john john 4096 Apr 13 08:05 software-center
drwxrwxr-x 2 john john 4096 Jul 26 2013 sso
drwx------ 3 john john 4096 Oct 27 13:04 telepathy
drwx------ 5 john john 4096 Oct 19 16:01 thumbnails
drwx------ 3 john john 4096 Oct 7 2013 thunderbird
drwxr-xr-x 3 john john 4096 Aug 4 2013 transmission
drwxrwxr-x 4 john john 4096 Jul 29 2013 ubuntuone
drwxrwxr-x 2 john john 4096 Jul 26 2013 unity-lens-photos
drwxrwxr-x 2 john john 4096 Apr 13 08:06 unity-lens-video
drwxrwxr-x 2 john john 4096 Jul 26 2013 update-manager-core
drwx------ 2 john john 20480 Apr 8 07:19 upstart
drwx------ 2 john john 4096 Nov 23 09:27 wallpaper

/home/john/.cddb:
total 20
drwxrwxr-x 3 john john 4096 Nov 17 2012 .
drwxr-xr-x 121 john john 12288 Apr 12 07:39 ..
drwxrwxr-x 2 john john 4096 Nov 17 2012 folk

/home/john/.cddbslave:
total 28
drwxr-xr-x 5 john john 4096 Dec 27 2011 .
drwxr-xr-x 121 john john 12288 Apr 12 07:39 ..
drwxr-xr-x 2 john john 4096 Dec 27 2011 classical
drwxr-xr-x 2 john john 4096 Dec 27 2011 country
drwxr-xr-x 2 john john 4096 Dec 27 2011 folk

/home/john/.compiz:
total 28
drwx------ 3 john john 4096 Apr 28 2012 .
drwxr-xr-x 121 john john 12288 Apr 12 07:39 ..
drwx------ 2 john john 12288 Apr 3 08:21 session

/home/john/.compiz-1:
total 28
drwxrwxr-x 3 john john 4096 Oct 14 2011 .
drwxr-xr-x 121 john john 12288 Apr 12 07:39 ..
drwxrwxr-x 2 john john 12288 Apr 6 2012 session

/home/john/.config:
total 312
drwxr-xr-x 64 john john 4096 Mar 14 13:09 .
drwxr-xr-x 121 john john 12288 Apr 12 07:39 ..
drwxrwxr-x 2 john john 4096 Jun 26 2013 anjuta
drwxr-xr-x 2 john john 4096 Feb 19 14:00 autostart
drwxr-xr-x 3 john john 4096 Feb 20 07:15 banshee-1
drwx------ 2 john john 4096 Apr 1 10:40 brasero
drwx------ 5 john john 4096 Jan 22 09:15 chromium
drwxrwxr-x 4 john john 4096 Apr 27 2013 Clementine
drwx------ 3 john john 4096 Dec 13 2010 compiz
drwx------ 3 john john 4096 Aug 1 2011 compiz-1
drwx------ 2 john john 4096 Apr 13 10:07 dconf
drwx------ 6 john john 4096 Jul 22 2013 deluge
drwx------ 2 john john 4096 Dec 15 2010 desktop-couch
drwx------ 2 john john 4096 Mar 18 2012 Empathy
drwx------ 2 john john 4096 Dec 14 2010 enchant
drwx------ 2 john john 4096 Apr 9 09:24 eog
drwxr-x--- 3 john john 4096 Dec 21 2012 epiphany
drwx------ 2 john john 4096 Apr 12 08:40 evince
drwx------ 9 john john 4096 Feb 18 14:34 evolution
drwxrwxr-x 2 john john 4096 Apr 16 2012 fbn.cx
drwxrwxr-x 2 john john 4096 Jun 9 2012 fmit
drwxrwxr-x 3 john john 4096 Nov 26 2011 gbrainy
drwxr-xr-x 2 john john 4096 Mar 14 13:12 gedit
drwxr-xr-x 3 john john 4096 Oct 14 2011 gnome-control-center
drwxr-xr-x 3 john john 4096 Dec 13 2010 gnome-disk-utility
drwxr-xr-x 4 john john 4096 Dec 27 2010 gnome-mplayer
drwxr-xr-x 3 john john 4096 Dec 13 2010 gnome-session
drwxrwxr-x 5 john john 4096 Jun 29 2013 gnome-sudoku
drwxr-xr-x 2 john john 4096 Oct 14 2011 goa-1.0
drwx------ 3 john john 4096 Jan 9 2012 goobox
drwx------ 2 john john 4096 Apr 13 08:04 gtk-2.0
drwx------ 2 john john 4096 Apr 3 08:22 gtk-3.0
drwxr-xr-x 2 john john 4096 Aug 15 2012 gwibber
drwx------ 3 john john 4096 Dec 13 2010 ibus
drwxr-x--x 7 john john 4096 Nov 23 2011 inkscape
drwxrwxr-x 2 john john 4096 Jun 29 2013 keepassx
drwxr-xr-x 2 john john 4096 Oct 18 14:28 libaccounts-glib
drwxrwxr-x 3 john john 4096 Nov 5 2012 libglabels
drwxr-xr-x 2 john john 4096 Dec 27 2011 libimobiledevice
drwxrwxr-x 4 john john 4096 Apr 27 2013 libreoffice
drwxrwxr-x 2 john john 4096 Dec 17 2012 lottanzb
-rw-r--r-- 1 john john 1124 Feb 1 16:37 monitors.xml
drwxr-xr-x 3 john john 4096 Oct 4 2011 .mono
drwxr-xr-x 2 john john 4096 Aug 1 2011 MusE
drwxr-xr-x 2 john john 4096 Apr 3 08:22 nautilus
drwxrwxr-x 2 john john 4096 Dec 17 2012 OpenTeacher
drwxr-xr-x 2 john john 4096 Feb 6 13:11 Pictopotamus
drwx------ 2 john john 4096 Apr 26 2013 pulse
drwxrwxr-x 2 john john 4096 Jul 15 2013 qBittorrent
drwxr-xr-x 3 john john 4096 Mar 14 17:48 QtProject
drwxr-xr-x 2 john john 4096 Dec 15 2010 rockbox.org
drwxrwx--x 2 john john 4096 Feb 4 08:01 signond
drwx------ 2 john john 4096 Dec 9 2012 Skype
drwxr-xr-x 4 john john 4096 Dec 13 2011 smplayer
drwxr-xr-x 2 john john 4096 Apr 13 08:11 software-center
drwxr-xr-x 2 john john 4096 Jan 20 2013 sound-juicer
drwxr-xr-x 4 john john 4096 Oct 4 2011 tomboy
drwx------ 2 john john 4096 Apr 13 08:11 totem
drwxr-xr-x 5 john john 4096 Apr 3 07:55 transmission
-rw-r--r-- 1 john john 34089 Feb 20 13:06 Trolltech.conf
drwx------ 2 john john 4096 Jan 6 2011 ubuntuone
drwx------ 2 john john 4096 Nov 17 2012 update-notifier
drwx------ 2 john john 4096 Oct 18 14:24 upstart
-rw------- 1 john john 632 Dec 13 2010 user-dirs.dirs
-rw-r--r-- 1 john john 5 Dec 13 2010 user-dirs.locale
drwxrwxr-x 2 john john 4096 Mar 8 10:04 vlc
drwx------ 2 john john 4096 Jan 15 2012 xfburn
drwxr-xr-x 2 john john 4096 Apr 10 20:42 yelp

/home/john/.cups:
total 20
drwx------ 2 john john 4096 Dec 9 2011 .
drwxr-xr-x 121 john john 12288 Apr 12 07:39 ..
-rw-rw-r-- 1 john john 82 Feb 10 16:30 lpoptions
john@john-p7-1109:~$

john@john-p7-1109:~$ sudo ls -la /home/john/.cache/
[sudo] password for john:
total 188
drwx------ 36 john john 4096 Mar 12 09:24 .
drwxr-xr-x 121 john john 12288 Apr 12 07:39 ..
drwxrwxr-x 3 john john 4096 Jul 28 2013 banshee-1
drwx------ 3 john john 4096 Aug 14 2013 chromium
drwx------ 2 john john 4096 Apr 3 08:22 compizconfig-1
drwx------ 2 root root 4096 Mar 12 12:09 dconf
drwxrwxr-x 3 john john 4096 Apr 10 03:17 deja-dup
-rw-r--r-- 1 john john 16384 Apr 2 07:32 event-sound-cache.tdb.436c9acdabeec30cab24765c51f2a1ee.i686-pc-linux-gnu
drwx------ 9 john john 4096 Oct 22 14:03 evolution
drwx------ 3 john john 4096 Oct 27 13:04 folks
drwxr-xr-x 2 john john 4096 Jan 10 16:17 fontconfig
drwx------ 3 john john 4096 Aug 1 2013 gegl-0.2
drwx------ 2 john john 4096 Oct 28 13:18 gnome-screenshot
drwxrwxr-x 2 john john 4096 Apr 13 08:04 gstreamer-1.0
drwxr-xr-x 3 john john 4096 Oct 18 14:24 ibus
drwx------ 3 john john 4096 Jul 26 2013 indicator
drwx------ 2 john john 4096 Jul 26 2013 indicator-appmenu
drwxr-xr-x 2 john john 4096 Oct 18 14:25 logrotate
drwxrwxr-x 4 john john 4096 Jan 11 15:52 media-art
drwx------ 3 john john 4096 Jul 26 2013 mozilla
drwxrwxr-x 3 john john 4096 Jul 26 2013 oneconf
drwx------ 3 john john 4096 Jul 28 2013 rhythmbox
drwxrwxr-x 3 john john 4096 Jul 31 2013 shotwell
drwxr-xr-x 3 john john 4096 Oct 25 18:52 signon-ui
drwx------ 3 john john 4096 Oct 20 08:26 simple-scan
drwxrwxr-x 8 john john 4096 Apr 13 08:05 software-center
drwxrwxr-x 2 john john 4096 Jul 26 2013 sso
drwx------ 3 john john 4096 Oct 27 13:04 telepathy
drwx------ 5 john john 4096 Oct 19 16:01 thumbnails
drwx------ 3 john john 4096 Oct 7 2013 thunderbird
drwxr-xr-x 3 john john 4096 Aug 4 2013 transmission
drwxrwxr-x 4 john john 4096 Jul 29 2013 ubuntuone
drwxrwxr-x 2 john john 4096 Jul 26 2013 unity-lens-photos
drwxrwxr-x 2 john john 4096 Apr 13 08:06 unity-lens-video
drwxrwxr-x 2 john john 4096 Jul 26 2013 update-manager-core
drwx------ 2 john john 20480 Apr 8 07:19 upstart
drwx------ 2 john john 4096 Nov 23 09:27 wallpaper

Hope that makes sense and thank you for your help

ok, as you can see all directories and files below .cache are owned by john:john, just dconf is incorrectly owned by root:root.

what is the output of
sudo ls -la /home/john/.cache/dconf

I just tried on my own system: Deleting the .cache/dconf directory did not create any problem, and the directory (and the file inside) were re-created after the next logon.

sudo rm -rf /home/john/.cache/dconf

john@john-p7-1109:~$ sudo ls -la /home/john/.cache/dconf
[sudo] password for john:
total 8
drwx------ 2 root root 4096 Mar 12 12:09 .
drwx------ 36 john john 4096 Mar 12 09:24 ..

Have deleted the .cache/dconf directory as you suggested

Thank you for your help
John