In last weeks update, we fixed a part of the Unread Query piece which wasn't doing things quite right. So it could be that some of those older threads that should've shown up before (with unread applied) are finally showing up correctly. Let us know if you continue to experience unexpected behavior with Unread.
Ah - interesting point. I hadn't considered that the earlier behavior could be the incorrect results. I'm slogging through the responses that show up. I'll eventually catch up...