It's a feature issue. the performance thread is strictly for performance issues - aka, does the site load quickly, or slowly? That's pretty much all it's for.
As for your problem, try hitting "mark all messages read" and report back. I might suggest hitting "all unread topics" first.
I can read every post, one at a time, slowly in a given thread, and it still puts me back at 9:30 this morning as the last post I've read. If it's a feature issue, then you must have gutted the feature since I left work at 5:30 pm this afternoon? Because it worked well until then.