I realize that this is an old thread, and I apologize for bumping it. But this is the number 1 search engine result for this problem, and I figured I'd add some additional information since I just encountered this problem.
1.) Make sure that Thunderbird is actually closed! Go into the Task Manager->Processes tab in Windows, or a system process monitor for Linux, and make sure that there is no entry for "thunderbird" or "thunderbird.exe." I have had this problem twice now, once in Windows 7, and once in Linux. If you don't completely close Thunderbird, then it will restore your profile when it finally shuts down and/or restarts. This leads to massive frustration, and/or the suspicion that your Thunderbird install is possessed and is knowingly trying to drive you to the brink of insanity.
2.) If you are using Linux, the equivalent folder to "
C:\Users\<username>\AppData\Roaming\Thunderbird" is "
/home/<username>/.thunderbird"
3.) If you have multiple mail accounts, you should follow Shadowajohn's advice, otherwise it will delete all of your mail accounts. You want to enter the "
xxxxxxx.default" folder, and then either "
ImapMail" or "
Mail" folder (ImapMail for IMAP accounts, and Mail for POP3 accounts). You then can delete only the directory that is causing you the problem. For example, my problem was with an IMAPed GMail account, so I deleted the "
imap.googlemail.com" folder in "
xxxxxxx.default/ImapMail".
