It is sort of a techy thing.
If you clicked on a thread that you watched, you are taken straight to that thread. So, the system knows that you've seen that thread.
However, that thread is technically different that the forum as a whole. So, where you have your list of watched forum, the system is still patiently waiting for you to click on that link (which would take you to the main page of the forum). It doesn't check to see if there are any other new threads, it only knows that you didn't click on that link.
As the site gets busier, this is less of a problem because there are always new threads and posts besides the one that you are watching.
