Comment 28 for bug 625670

I was also experiencing the problem. Looking at the workaround that involves killing gnome-settings-daemon, I guessed that it's being caused by the instance of gnome-settings-daemon that was run with gdm's gconf settings not shutting down properly before another instance of it was run with the user's gconf settings. So I added the line "killall -9 gnome-settings-daemon" to /etc/gdm/PostLogin/Default to make sure gnome-settings-daemon is killed when the user logs in, and this seems to have resulted in the desired behavior: the user's theme is applied correctly after logout and login, and gdm doesn't lose its own theme.