After you maked them as read, did it say there where no new posts?
If you click 'mark posts read' it will set the date to the last time you clicked it/logged in. So all posts made between the last login/click and now will still be shown as unread. This is because it would otherwise be very easy to miss a post because it was made just after you read a thread.

What was the new post count of that thread? Where there actually that many new posts? did it jump to the correct post?

I did notice a bug where the link would jump you to the wrong post, so you ended up at a post two up from the newest one. Could that be the problem here?