Profile problems - loosing bookmarks

I use Firefox 3.5 with a 'home' profile and IE 7 with 'work' profile. Twice in the last two days my home profile has lost the items in the Bookmarks Toolbar folder that are included in both profiles. I have managed to rebuild from a previous xmarks backup (thanks for providing access to the backups).
Any ideas what I might be doing wrong. At work I often get the Xmarks 'known problem with IE' pop-up and I always click 'Cancel.