Odd slow behaviors going on

It is hard to describe what exactly is the problem, but on a newly rebuilt machine some things are darned slow.

I just rebuilt my Gutsy i386 machine as Hardy Beta amd64 using the xubuntu distro. flavor. Everything at that time seemed relatively okay, but I have not been running it long to say for sure.

Yesterday (or Sunday morning - the 30), I installed the latest updates through apt, and I am having a lot of problems, all of which are hard to point a finger at. I cannot remember the exact packages that were upgraded, but I have attempted to rebuild the list from the apt log file (see below). I am seeing not only some X instability (a lot of crash dialogs popping up), but some general slowness problems. For example, nut-cgi requests to a running upsd on the same box keep timing out, but I cannot see any log information that would hint for what is going on. On xfce4 startup, I launch mail-notification. It takes about 5 min for the icon to show up in the system tray. If I start mail-notification from the command-line, it runs with no output, but the UI just does not come up for a very long time.

I am not running compiz at the moment, so despite its upgrade it should not be having an effect to my knowledge.

Apt log (filtered):
2008-03-30 06:22:01 upgrade libgtk2.0-common 2.12.9-2ubuntu1 2.12.9-2ubuntu2
2008-03-30 06:22:01 upgrade gtk2-engines-pixbuf 2.12.9-2ubuntu1 2.12.9-2ubuntu2
2008-03-30 06:22:02 upgrade libgtk2.0-0 2.12.9-2ubuntu1 2.12.9-2ubuntu2
2008-03-30 06:22:04 upgrade guidance-backends 0.8.0svn20080103-0ubuntu8 0.8.0svn20080103-0ubuntu9
2008-03-30 06:22:06 upgrade libgtk2.0-bin 2.12.9-2ubuntu1 2.12.9-2ubuntu2
2008-03-30 06:22:06 upgrade xfce4-quicklauncher-plugin 1.9.4-1ubuntu2 1.9.4-1ubuntu3
2008-03-30 06:22:06 upgrade xserver-xorg-input-wacom 1:0.7.9.3-2ubuntu2 1:0.7.9.8-0ubuntu2
2008-03-31 15:39:00 upgrade xkb-data 1.1~cvs.20080104.1-1ubuntu2 1.1~cvs.20080104.1-1ubuntu3
2008-03-31 15:39:00 upgrade libparted1.7-1 1.7.1-5.1ubuntu8 1.7.1-5.1ubuntu9
2008-03-31 15:39:01 upgrade openssh-server 1:4.7p1-5ubuntu1 1:4.7p1-6ubuntu1
2008-03-31 15:39:02 upgrade openssh-client 1:4.7p1-5ubuntu1 1:4.7p1-6ubuntu1

Now, I am using an old version of nut, so I am going to ignore that for now (nut 2.2.1 is not compatible with my UPS at the moment). All my other problems seem to be with the UI. When I did the above upgrades, my Xfce4 sessions were corrupted. xfce4-panel would no longer start automatically, and when it did start all my icons were missing. I had to purge my .local, .cache and .config user directories to repair things. Furthermore, other tray icons were having problems. For example, knotes would start a little window instead of creating the tray icon. The same problem happened with knutclient.

It seems as if it may be gtk related, but I am not sure at all. Most of the slowness all happens around the tray icons. After starting a new xfce session with those local folders deleted, knotes and other k* tray icons start fine, but mail-notification is still really slow.

Anyone have an idea of what is going on or similar experiences? If you have similar experiences, are you on amd64 too, or is this also happening on i386?

Thank you,
Andrew