The way the software works should be the same as it was before... clicking on the link where you have unread posts should take you to the first unread post but clicking on a link with no unread posts will take you to the first post in the thread.
That should be how it's working, it should be taking you to the first post that it thinks you haven't read yet. It's possible that when the software was upgraded and the cookies cleared that it reset the counters for some but that's a theory I'll need to verify.