Messages can only be archived manually, not automatically.

Wrt the disappearing mail see http://kb.mozillazine.org/Disappearing_mail

I have disabled all archive settings in Account Settings, Copies and Folders for each account.

I disabled all filter on the account.

On config editor, I set all achive_enabled to false. But later on the value back to true by it self, on a Gmail IMAP account.

And the email still coming to the unwanted archive folder.

Any idea how to stop this behavior ?

I had this problem and found it was due to a filter I had put in Gmail - the messages were being archived by Gmail before being downloaded by Thunderbird.

I too have the same problem and have done everything mentioned above--TB still AUTOMATICALLY archives to ALL email accounts, not just Gmail. Plus, in one account (a gmail account) it shows thousands of emails have been archived, but does not display any at all.