Why won't my Firefox display my Bookmarks?

I reformatted my computer and backed up the whole folder that Firefox stores in the application data folder in vista, but when I try to reinstate the bookmark backups that Firefox made they won't load into the Bookmark Manager or the Bookmark drop-down list. However, they do show up in the auto-fill address bar feature. Like, if I type a website, it comes up with my bookmarks that I have for that site and different pages of that site, pages I've never been to on this new Vista install. I tried reinstalling but it didn't change anything. Whats wrong?