I have tons of "new" unread threads, too, but most watched threads are still correctly marked as read. I'll check the most recent ones and then mark everything as read unless Greg wants data to investigate. It looks like it's time- and subforum-dependent.
No change (kept marked as read):
* feedback, aerospace engineering
* all threads with a last post older than exactly 1 year independent of forum
Now unread:
general discussion, high energy physics, electromagnetism, calculus and beyond homework, astronomy and astrophysics, nuclear engineering, general math, ... looks like most forums