it's not really "unread threads", it's "threads with new posts since last visit."
"Last visit" is a relative term in this case. If the threads are showing up "new posts" when you get there, then you spend time reading, writing, or otherwise dallying, the next time you click through your current visit has become your "last visit."
Basically, if a certain amount of time has passed all of those threads that were listed as "new posts" will be listed as "no new posts"