I am suffering from a strange problem with my Gnome Shell in Ubuntu 12.10.

1. The login takes very long (> 30 sec), with a blank screen.
2. In Google Chrome and Thunderbird (and perhaps in other applications), the main window freezes and is repainted in periodic intervals of less than one minute. The freeze takes several seconds, and it seems that font and appearance of, e.g., tabs and buttons briefly changes.
3. Attempting to enable the second monitor show an error message related to XRANDR.

Everything seems to have started three days ago, after I had to force-shutdown the machine while it was hibernating due to low power. (It was hibernating for quite a while and didn't want to stop.) Silly me.

I have tried the following measures, with no avail:

1. Checked all package file md5 hashes using debsums
2. Reinstalled all packages using a variant of dpkg --get-selection \* | xargs apt-get install -reinstall
3. Temporarily moved configuration directories such as .gconf, .config and .gnome2 to another location
4. Created a new user account

When I choose "Ubuntu" during login, the problems disappear.

I am sort of frustrated that reinstalling all packages didn't fix the issue. How to troubleshoot this Gnome Shell (?) problem, short of reinstalling the system? (Or did anyone see this kind of behavior on their machine?)