It's harder to instruct someone online, so here goes...
Any kind of pop-up blocker software, including the Google pop-up stopper, will only block the stuffs coming from the visiting website, but if the pop ups orginated from inside your PC, Google will be helpless.
So, how often do you get these popup? Do you get it while visiting a website? Or it just pop up as soon as you open a browser windows (the latter is more serious)? I can go on and on to tell you what to do, but maybe it's best if we go from step to step.
..rb