Firefox 2.0.0.9 but I also have had older verses and had the same problem
Firefox cashes the bookmarks and writes them to the hard drive when it is closed properly. If you leave Firefox running and sleep or shut off your computer without shutting it down, Firefox may not have time to finish writing the file before the computer turns off. That is essentially a crash and the file may be partially written or the directory entry may be corrupted or the file contents may be corrupted. Firefox creates a new bookmark file when it cannot find a good bookmark file.
Firefox also creates a bookmarks.bak file. Next time this happens, go to the Application Data directory for mozilla\firefox ... for your profile and copy the bookmarks.bak to the bookmarks.html file. That should get you back. That needs to be done with Firefox not running.
But the best advice is to close Firefox before loging out or shutting down your computer.
As a safeguard, you can open the "Organize Bookmarks" dialog and under the File there should be an Export and an Import option. Export a copy to your Documents directory.
As a note, you can synchronize bookmarks between accounts or computers by just copying the bookmarks.html file from one account to another. That needs to be done with Firefox not running.