On your firefox shortcut, add a -p to the end of it. It lets you select your profile. A new one probably got made, and your bookmarks are in the other one.
Or you can look in C:\Documents and Settings\<username>\Application Data\Mozilla\Firefox\Profiles and see if theres more than one profile directory. If so, look in each one and you'll see bookmarks.html. One of them will have all your old bookmarks in it.