Rich Bowen remarks that he sees Apple Mail flip recently read messages randomly back to unread status. I am seeing this too and it bugs me.
I searched Apple’s support discussion forums and turned up a discussion on this very topic. It seems the Apple engineers blame the issue on ambiguities in the protocol standard, but one would expect that at least between Apple’s own .Mac mail the client-side and server-side interpretations of the standard would lean the same way.
Another interesting data point is the closing post of the thread, blaming the GPG plugin. I, too, have that installed. I may pull it and see if the problem goes away. I think Apple should support PGP directly in Mail.app anyway, right alongside S/MIME.
I’ve been using Apple Mail.app since years now with quite a lot of accounts and messages (POP & IMAP) and I’ve only experienced this once with a kind of broken IMAP server – so I’d suggest to simply try another one (*) and see if it fixes your problem. I’ve been running courier (over tls/ssl) for a while now w/o any issues whatsoever…
Cheers,
Erik
(*) I know that might not be that easy but it might be worth a try.