just updated my system. While this was in process, I tried to switch compiz to metacity (checking for another bug). The X-server froze and I switched to tty2 to stop gdm. This took a long time and afterwards even the Xorg process hang. I entered reboot, but the system could not reboot in the last third of the stop procedure. I used SysRequest+s, -u, -b.
After reboot I saw: /home was unmounted unclean, check forced.
When I came into gnome again, my compiz settings were partially cleared and my gnome-terminal settings were lost. I can not say, if the files were zero bytes. But maybe the e2fsck had corrupted some files.
The updates that had taken place did not include compiz or gnome-terminal so at this point I can not see a connection to the updates done and the lost information.