Jacob,
I like Firefox. I've been using it for a few years. Try this:
http://kb.mozillazine.org/Lost_bookmarks
or one of these:
http://home.att.net/~cherokee67/fflostbkmk.html
http://mozilla.gunnars.net/firefox_book ... orial.html
Last chance:
C:\Documents and Settings\user_name\Applicationdata\Mozilla\Firefox\Profiles\random_characters.default\bookmarkbackups\
This is where Firefox 2.0 keeps backups in WinXP on my computer ("user_name" and "random_characters" will be different on every computer). I try to make my own backup every time I make a big change to the file.
If you see the bookmarks are different, do not quit Firefox. Go make a copy of the bookmarks.bak file and rename it. Then change the extension of the renamed file to .html and open it with Firefox and see if has the locations you want.