Threads I have posted on sometimes appear in my watchlist and sometimes they don't. Also, my watchlist currently says there is a new post in a thread I am following and when I hover over it, nothing loads. Clicking to go to the full watch list shows there is no new post but doesn't fix the problem with the box turning blue and displaying a 1.

Same here. Watch list is definitely not working properly. I started a thread and it doesn't even show up on my watch list at all.