IE 7 ?My favorites? keep disappearing.

In our department, Staff member have lost all their Favorites. It has not happen again but we are trying to figure out why they got deleted. Two scripts were written and pushed from our server last week so that the PC?s will shut down before midnight and the other to bring up a screen saver after 20 min. of inactivity. We checked both scripts several times but found no errors. Anyone have any suggestions?