Just had this same problem.
Firefox updated itself and voila: Bookmarks are gone.
What's really weird though is that I had put some bookmarks into special sub folders. The subfolders are still there. Anything that wasn't in a subfolder though (most of my bookmarks) are gone.
I tried the safemode thing... didn't work unfortunately.
Tried the line above as well. I wasn't able to solve anything via that way either. I'm not sure if I should start my own thread on this as I would be asking the same question.
It seemed as though Firefox just updated itself on my machine and killed the bookmarks. I'm running 126.96.36.199 now. Any advice is welcome because those bookmarks will be impossible to get back otherwise.
Edited by videoguy, 05 November 2008 - 03:22 PM.