Has there been a new release today. Today i ran it and all my bookmarks are gone.Also a box came up and it asked about my profile.
I did notice 1.5 rc2 was released yesterday. http://www.mozilla.org/projects/firefox/ Not sure that would be the problem though.
Maybe your profile has become corrupt and you need to create a new one. I would ask at the Mozilla Firefox forum though if no one can answer you here. You don't even have to join the forum to post a question. http://forums.mozillazine.org/viewforum.php?f=38 Best of luck solving your problem.
I'm still using v1.0.7... the 1.5 RC scares me a little, as I'm not a tecno geek maybe I have to wait for their final release to avoid problems.
I noticed this happens with beta/alpha/RC releases sometimes, so I put the Beta in a new folder. Add beta or something to the folder name to keep it seprate form my regular Browser and copy favorites manually as I need them.