Firefox 3.6.12 is deleting all my profile data once per day on Windows Vista. 3.6.11 worked fine.
09.11.2010 After an autoupdate to 3.6.12 Firefox asks for profile when starting up. Firefox does not recognize existing profiles in the correct profile directory. Bookmarks etc are copied to a new profile and the new profile taken into use.
11.11.2010 Firefox starts up by asking for profile. All previous profile data has been deleted. The only thing remaining is a > 46MB big urlclassifier3.sqlite file in the local\firefox\profiles directory. All bookmarks, cookies and other information has been deleted from all previously defined profiles(!!!)
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This can happen if you have uninstalled a Firefox version and placed a check mark to remove personal data. That will delete every profile folder listed in profiles.ini, also from other versions.
See also http://kb.mozillazine.org/Recovering_a_missing_profile