There's been a ton of discussions about these very issues. I suffered the same problems when i loaded 1.0. Check for the bookmarks under the mozilla firefox bookmarks.html file. They may be there. It is also possible that you may have inadvertantly exported them to your IE favorites.
Go to Mozilline forums.
http://forums.mozillazine.org/.
Do a search there. You will find an enormous amount of info about this very issue. The new Bugzilla i belive addresses this issue as well. (at least i think it does). good luck.
edit- your bookmarks ARE there. You didnt lose then. You just have to hunt and peck around to find them.