I think I've got it figured out - at least for me. When I excluded the 'MessageUidsAlreadyDownloaded3' file from the Time Machine backup, the duplicate problem went away (for now) I will re-post if it recurs. This makes a lot of sense to me now. If Time Machine continuosly backs up the 'changed' files on the Mac, and the 'MessageUidsAlreadyDownloaded3' file is changed every time Mail is checked, it will constantly be getting backed up. During the back-up, the file is locked, so it can't be accessed by the Mail program when it is checking for new mail, so the Mail program simply re-downloads everything and the whole cycle starts over. By excluding the file from the back-up, it will no longer be locked, so Mail will be able to access it.