I've been having the same problem: it's a blue bouncing ball that pops up only on FT (and sometimes has a matching banner ad at the top of the page) and prevents me from reading posts. Changing my pop-up blocker setting to "high" doesn't solve the problem at all--it seems to pop up just as often--but inconveniences me when I want to click on links. I think this has been happening constantly for about the last couple weeks and I haven't noticed that it's correlated with the forum I'm using.

For the record, I use IE with Windows XP and run up-to-date anti-virus/security software.