Regarding that popup box when there's a thread with new posts., one of two things are likely to happen for me when I mouse over it. The first is, my cursor will change (to a hand? I don't recall at the moment and have no new posts to test it on). It'll change to say there's an active link under here and if I click, I will /mostly/ always end up on the first unread post.
However sometime the cursor won't change and if I click on the box there's no telling where the hell in the thread I'll end up. By paging back then ahead, I can usually get the correct cursor.
But even then it doesn't always work right especially if the new post is on a brand new page. And sometimes the page won't load and be completely greyed out.
tl;dr - Be happy it works at all.