I too am sorry for the confusion.
We made a change to the way the forum figures out which threads you're read and which you haven't. The way it was previously set was the least accurate method, and doesn't provide the best user experience. The method we're using now is extremely accurate.
Obviously, when the change is first made, the forum doesn't know which you've read and which you haven't. It apparently makes the assumption that you haven't read any threads for a specific period of time.
This side effect was not expected by us, and we are sorry for the inconvenience. Had we anticipated this, we would have posted an announcement and looked for ways to mitigate against it before making the change. We did notify the moderation staff that we were going to make the change, but even they were taken by surprise when this unexpected result occurred (IBsteph included, hence the confusion).
This change was made because we believe it should offer a better user experience. If we had expected a change in functionallity that was this drastic, we would have not made it without much more warning. Once again, we are terribly sorry for the inconvenience.
On the front page, there is a button that says "Mark Forums Read" that will mark everything read. From this point on, the read / unread status of every thread should be completely accurate. This can also be done on a per-forum basis by going to the forum homepage and clicking on the forum icon.
Since this change had such drastic results, we are still considering rolling back. We are working with the moderation staff to come up with the best solution.