I am having the same issue.. thousands of incoming messages under the mail activity header on the lower left of mail. I mean THOUSANDS. And I can't find any of them. All of the messages are current or empty in each mailbox and I have reset everything where it won't archive or save anything. I have no idea whats causing it. Very strange. It continuously does this through out the day. But where are these emails? They aren't in my inbox, trash, archives, etc. of any of my mailboxes. Has anyone solved this yet?