Just lost a day to this myself (though my fault for not keeping backups).
A permissions (or configuration, I suppose) error anywhere in the gconf hierarchy can turn this up.
In my case, /etc/gconf/2/path included references to the following (installed automatically at some point):
As it turned out, /var/lib/gconf/debian.defaults was not world-readable.
The only clue logged regarding this was:
The files that contain your preference settings are currently in use.
You might be logged in to a session from another computer, and the other login session is using your preference settings files.
You can continue to use the current session, but this might cause temporary problems with the preference settings in the other session.
Do you want to continue? Continue (y/n)
in /var/log/gdm/:0-greeter.log. Not exactly the first place I would look, or the clearest indication of where the problem is. (After numerous attempts to reinstall and reconfigure all related packages, I was hunting for lockfiles...)
IIRC it looks like fresh installs (or 100% fresh installs of gconf) may not include /etc/gconf/2/path at all (or delete it?), so the wrong permissions from whatever package installs /var/lib/gconf/debian.defaults may only turn up for upgrading users.