Try going to the first index page of each discussion area and clicking the "Mark Read" tab on the upper right. Warning: this will flush all the markers for currently-unread posts, so read the new posts you're interested in before you do it. (You should only have to do this once to fix the problem.)
(When asked to fetch unread messages, the forum software seems to look for a contiguous group of chronologically-newest posts at the top of each index. But if you missed one or more discontiguous messages earlier --they could be 2 or 3 pages down in the index, where you haven't noticed them-- it can screw up the fetching of unread messages. Marking everything as read usually fixes this.)