Why do I get false new mail alerts when I know that I have no new mail?
Even after I have read all new mail and deleted those I do not want to save from the server, I get a new mail notification. This has been going on for a few years now, however quite some time ago it did not happen. I have a suspicion that when Thunderbird does a mail check and there has been a recent deletion of mail, it registers as new mail. Seems it may be confused on the direction of the mail with regard to the mail server.
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You're confident that there are no new messages that went directly to Trash or Junk, or were moved by a filter?
Does View|Folders|Unread show up any unread messages hiding in unexpected places?