There are a couple of types of popup.. There is also the Windows style Message box.. If you are not on a network, you can disable the "messenger" service from the Services section.. Hope it helps.
Keep in mind, that there are 2 types of pop-up adds. Most software packages only block the ones that attempt to open a new browser window. For the MSN Messenger pop-ups, you need a different solution.
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pop ups
Thanks,
Michael