We're having the same thing happen at
Manic Geeks since the installation of the 0.8 upgrade. One way to get rid of it, although it's not a fix nor is it permanent, is to go to the bottom of the unread messages list, select "Visible Discussions" in the "Mark as Read" box, and click "Go". The unread list will refresh properly at that point. Unfortunately, the problem comes back eventually. I haven't been able to see a rhyme or reason to it yet.