For some time now I have noticed that when I downloaded my e-mail I was seeing higher counts in the status bar than I was new messages in my inbox. When I first noticed the problem, one of my mail accounts was claiming to download 61 messages more than I was actually getting.
I am not sure when these phantom message headers appeared, or what may have caused them. I have managed to rid myself of them ( for now ) and I wanted to share the steps in case some one else is having the same issue.
My next step was to move the ~/Library/Caches/Mail folder to my desktop. This didn’t work either.
Finally I logged into the control panel for my account at my ISP and deleted the mail account from the server ( after downloading all the mail there first, of course ). Then I re-created the account on the server.
This steps seems to have worked. When I get my mail the status bar numbers match the instances of new mail in my inbox. Personally I think that an aborted or failed mail retrieval attempt left these headers on the ISP server somehow. Deleting the account there, with a seemingly empty inbox, got rid of problem when nothing done on my machine worked.