Well to get around this, i would do an old fashion trick i learned before pop-up blockers came along.
ok, when a I.E window pops up, right click the window/and go to properties.
get the location and copy it ,by right clicking it
example:"http://www.anoining popup.com"
then go to internet options in the control panel.
once there/ go to privacy tab/ then edit box.
then in the box on the top left : right click & paste...
then click the block box.
if you do this for every window that pop-up, you will get them all.....i know this may sound like a long way of doing it....but it works.
hope that helps.