I've seen this same issue come up in multiple threads, but this looks like the oldest, so I'll make my post here.
I've had 25 unread messages since the site relaunch. I didn't see this error in the site preview, and it wasn't an issue in the old site. I've went through and marked all messages (inbox and outbox) as unread and then read, but I'm still showing 25 unread. The unread section of my PM box is empty, despite the number staying at 25. This issue is consistent across other browsers and platforms after clearing cookies and cache.
This is obviously in no way an urgent issue, but as this has been going on for a while, I thought I'd report what I tried to do to resolve it.