Oh wow, so it checks for new posts since the last time you clicked to the forum itself. So when it shows the most recent thread, and you click the arrow, if you don't actually visit the thread listing, it will continue to show it as having new posts in the index.
For example, I click the Cross Site link, because I visit several of the forums contained within. The OOT has a new post since my last visit and it's in a thread I was interested, so I click the arrow next to the thread title to bring me to the first unread post. I finish reading the thread and I'm all done. I close the tab. Later, when I open a new tab starting at the Cross Site index, it's still showing a new post in the OOT since my last visit, because I never clicked to the OOT thread listing; I went straight to the thread and then finished my session.
This would explain my previous issue. It wasn't that I had posted in threads, it was that I had not been going back to the specific forum, but to the Cross Site forum listing. I'm assuming that currently it just compares the timestamp of the newest post in a forum to that of the user's last load of that forum index. Opening a thread doesn't constitute "visiting the forum" apparently.