When you lost your bookmarks, do you recall seeing a message pop up asking you to choose or create a profile? This happens if you quit Firefox, but the process doesn't end. When you try to start Firefox again, it sees that your profile is already in use and asks you to use another one.
I suspect that you have accidentally created a new profile. Find the old stuff as follows:
Quote:
* On Windows XP/2000, the path is usually %AppData%\Mozilla\Firefox\Profiles\xxxxxxxx.default\, where xxxxxxxx is a random string of 8 characters. Just browse to C:\Documents and Settings\[User Name]\Application Data\Mozilla\Firefox\Profiles\ and the rest should be obvious.
* On Windows 95/98/Me, the path is usually C:\WINDOWS\Application Data\Mozilla\Firefox\Profiles\xxxxxxxx.default\
* On Linux, the path is usually ~/.mozilla/firefox/xxxxxxxx.default/
* On Mac OS X, the path is usually ~/Library/Application Support/Firefox/Profiles/xxxxxxxx.default/
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There is some discussion as to how to make it more obvious to the end user that this is what happened; hopefully, it'll be better in version 1.1.