Probably permission Issue, maybe caused by Apps2SD
I've seen this issue a few times as well. Debugging this, it turned out to be the infamous permissions problem: The system had forgotten the mapping between user IDs and apps and had created a new mapping from scratch. If this happens, Android creates (or appends to) a logfile /data/system/uiderrors.txt listing the problems and the changes that were applied.
Typically, the symptoms are that (1) some user apps cannot access their data anymore and crash, (2) system apps have their data removed entirely (which is why you're asked to redo initial setup), and (3) user apps moved to the SD card with Apps2SD vanish in thin air. Uninstalling and reinstalling the user apps doesn't help because their data directories with the old, inaccessible UID remains in place.
A quick remedy for (2) is to manually run the fix_permissions script floating around this forum. Often it's still possible to runs this in the terminal emulator after this problem has occurred; or you could do it using adb (if debugging was enabled), or even automatically at each boot by calling it from /system/etc/install-recovery.sh.
In my experience, this issue occurs more often when Apps2SD is used. As an experiment, I have stopped using Apps2SD altogether and rely on Link2SD instead. This seems to have entirely fixed this problem for me.
Last edited by altruizine; 08-12-2012 at 04:52 AM.
Reason: Corrected title: issue might be caused by Apps2SD, not Link2SD