If you try importing an existing profile into your current profile by copying over the current profiles settings, it'll do that. Ran into that problem a few times in XP, but never really associated it with copying the profile settings until it happened in Linux too.
Normally I back up the Mozilla and Thunderbird folders under Application Data (or .mozilla and .thunderbird under my /home/ folder in Linux) whenever I'm going to wipe the drive, and then copy/paste the backup's over the new installation. Works like a charm if you do it before you use the newly installed browser/mail, but if you fire them up first, and then copy the settings over afterwards, it gets all kinds of fucked.
Both Firefox and Thunderbird check for the existence of the Mozilla and Thunderbird folders. If they don't exist, they get created. If they do exist, they get used. It's so nice being able to migrate ALL your settings, extensions, installed plugins, bookmarks, email address books, mail, junk filters, mail filters, account settings, etc in one shot. I just have to remember to copy my old settings over before starting Firefox/Thunderbird up for the first time (of course if I should forget, it's a simple matter of deleting the Mozilla and Thunderbird folders, and then copying my old settings over again, to put everything back right)
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