Open suse kde 4.2. Thunderbird keeps mail for a few minutes and gone, vanished. Checked the account settings, nothing about delete or move. Never had trouble before.That’s it 
thanks
In account settings
Check the Disc space section settings
This may not be related to the behavior you describe, but when I first saw the following “feature” on my computer, I thought as you did, “My mail is disappearing!”
Unlike any email client I’ve used before with my gmail account, Thunderbird keeps synchronized with the the gmail server. I read my email on my BlackBerry (or another client computer) and sometimes delete it, which moves the email from the gmail inbox to the gmail trash. When my computer with Thunderbird next synchronizes, it sees the change at the gmail server and moves my mail from the inbox to the local gmail trash folder. There are local gmail folders on the Thunderbird client, and I can see that the mail that was just in my inbox has moved to the local gmail trash folder.
In your case, your email may be set to “delete” from server after download. So, Thunderbird retrieves mail from your server, the server moves all downloaded mail from the inbox to the trash, then Thunderbird synchronizes with the server and moves the recently received emails from the inbox to the local server’s trash folder to mirror what it sees on the server.
Make sense?