I'm in the same situation, about once a week this message appears with no apparent reason and some settings (desktop background, GTK+ theme, ...) are lost until reboot/logout. I think it might somehow be relevant that I am using autologin - I've heard of similar problems caused by something (dbus?) not loaded soon enough, before something else (gnome-settings-daemon?) when using autologin. I will try setting GDM to login after five second delay to see if it helps. Unfortunately, it will take a few weeks to say with reasonable accuracy if there is any difference.
I'm in the same situation, about once a week this message appears with no apparent reason and some settings (desktop background, GTK+ theme, ...) are lost until reboot/logout. I think it might somehow be relevant that I am using autologin - I've heard of similar problems caused by something (dbus?) not loaded soon enough, before something else (gnome- settings- daemon? ) when using autologin. I will try setting GDM to login after five second delay to see if it helps. Unfortunately, it will take a few weeks to say with reasonable accuracy if there is any difference.