This has occurred off and on in most versions of the client that I've used, from v6.5 thru 8.0.2, and is annoying. My experience has shown that this usually happens in instances where, upon receiving new mail, the message has been moved to another folder by a rule.
Sometimes standard database maintenance (fixup, compact) will take care of it, sometimes it won't.
You can use the All Documents view to figure out which messages are still flagged as unread.