I use either Internet Explorer or Google Chrome and I've had a few pop-ups blocked from RB, but not very often .... it's wierd that it's only occasionally though!!
I've run a virus scan on my computer and my laptop's clean, so I don't know what it is!! :?
RB certainly don't have any pop up, pop under or pop across ads.
As Fluffy Chicken correctly says the odd one appears when you click an externally hosted pic from the external host - this is not in the control of RB. You may also get false positives with the ebay links due to forum code affiliating (i.e. modifying) them.
FC, I don't think it's pm's popping up, as they show up anyway.
Maybe it is just as John says, that it's external stuff, I'm not worried about it though, as it only happens very rarely.