Have a read of
this it may help. Looks like some cleaner programs can remove the bookmarks.
I use ccleaner set to run on startup and so far have never had a problem with firefox bookmarks.
Although I have had the select profile window come up from time to time after running some vid clips from the web. and shutting down firefox then trying to reopen it, This is normaly cleared by the old ctrl/alt/delete and looking for the firefox .exe thats running and closing it down. Then trying again.
Max