Bug#443792: I've seen these issues. Looks to be gconf related.

[James LewisMoss]

When I've logged out of X and logged back in, but not when logging in
right after a reboot.

It looks like the gconf daemon doesn't exit properly when X exits so the
next time you start there are two running, but the new daemon can't
access the gconf db (probably the old one has it locked) so it gives
back empty/invalid/missing config values.

This causes all sorts of problems for the new programs starting up.

If, when I log out of X, I go to a text terminal and make sure to kill
the gconf daemon before logging in to X again I never see the problem.

Jim

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