Ok, the problem isn't just the indicators now. I just went to the General SW forum and hit "Unread posts" on a thread I was in last night and it brought me back to the first unread post from over a week ago when the thread started (in case it makes a difference, it's the "Our Fault, Not George's" thread).
I'm using Firefox 3.5.3 but I upgraded to it before you upgraded the forum recently, and since this thread indicator issue only started for me in the past couple of days, I'm guessing the browser isn't the culprit.
Also, I just fired up the forums in IE, which I hardly ever use, and IT was even showing all the indicators white, nothing in blue, which means it thinks that everything has been read when, if I haven't used it in such a long time, the forums should come up as unread for the past few months.