I've had this happen to me too. All messages in inbox are read (or inbox empty) and I'd still have an unread message in folder view. Now I've got 2: I recently undeleted a trashed message, and wonder if that's what did it.

Refreshing email doesn't fix it. Emptying trash doesn't. I assume deleting and recreating the account would fix it, but I'm looking for a less destructive fix for what's really an annoyance, not a catastrophe.