If all of the ads are coming from the same server, add that server to your Windows HOSTS file and make it resolve to 127.0.0.1.

Dunno if the ads will pop up as empty windows or if they will not pop up at all...

You might also choose to use a different product to kill your pop-ups, something that doesn't slow down your CPU. On my Windows2K box, I'm using PopUp Ad Filter, but it doesn't work right on my Win98 box, so I don't know how to test against it.