I updated this thread:
http://ubuntuforums.org/showthread.php?t=1575703&page=2
but here's the short version.

I removed the sun-java6-plugin package, thinking it was the source of
the problem, but I continued to see random theme changes. Then I stopped
using Gnome-Do/Docky and went back to using the regular Gnome panel.
Since then, I haven't seen any random theme changes. My new plan is to
begin using Gnome-Do/Docky again to try and recreate the bug.

If successful, then I think the bug can be safely narrowed down to the
Gnome-Do/Docky package.

-- 
randomly gnome-settings-daemon fails to start
https://bugs.launchpad.net/bugs/588155
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