Have you tried clicking on the "View New Posts" link on the right side (when you're at the board index)? When you click there you can see which threads you've read and which are new. Anytime there's new posts in the thread it should show up as unread for you if you haven't read it.
The same should be true if you click the "View Active Topics" link. When you refresh that page, if a thread has a new post in it then it shows up as unread for you. If there's an orange box to the left of the thread then there is a new posts(s) in it and it's "unread." If the box is gray then you've already seen it and there's nothing new in the thread so it's "read."