Are you using Win XP with SP2? bcoz with that .. IE allows you to prevent most pop-up windows from appearing over pages.. (In IE :: Tools >> Pop-up Blocker >> Popup blocker settings)
But i remember reading that ... those "blocker" are smart enough to not block windows that are opened deliberately by us.
That said, anyway chk out wheather you are running any utility/app to block the popups.
Best Regards
Vadivel
MVP ASP/ASP.NET
http://vadivel.thinkingms.com