maybe it's already been reported but I got the console logs when mail is duplicating messages.
seems there are two messages sent to a class object in Mail.app:
-[SeenMessagesManager _accountForAccountID]
-[SeenMessagesManager saveChanges]
both are raising an exception about the fact that they cannot open, for some reason, MessageUidsAlreadyDownloaded3 file, despite the fact that the file is in place and have permissions.
it's a bug in Mail.app; the exception raised is localized (Italian in this case).
Mail tries hard to find this file, at least 10 times per second, for 4 seconds before probably giving up and redownload all the stuff.
My best guess is that this file become locked during certain processes and not accessible, but the error raised is pretty generic, it just says that cannot open the file, not why.