Fuck! It just did it to me right now on a forum running vBulletin 4.0.4. I am usually careful when reading those forums to avoid this problem, but I got distracted by some work emails and went about 20 minutes without touching the site. When I got back, all the threads were marked as read except those that had been posted in since I last clicked on something.
I HATE when that happens. Fucking vBulletin piece of shit software.