Came across a strange problem at work today. A Windows 7 32bit workstation that was recently upgraded to to IE 9 started exhibiting some strange behavior. All of the pop up window links (on any website) no longer worked. Clicking on a link that should open a popup window did nothing and displayed no error message. Other browsers were unaffected and correctly displayed pop up windows. Everything was functioning correctly for about two weeks after the upgrade so it didn't appear to be a failed upgrade. Unfortunately by the time the problem was discovered it wasn't possible to roll back to a system state before IE 9.
The problem was finally resolved by running the IE repair tool from Internet Explorer FAQ. The tool is a command script to re-register a long list of common controls that Internet Explorer depends on. After downloading and running the correct script (Right click, run as administrator) the problem was immediately resolved.
Hope this helps someone looking for an explanation why pop up windows in Internet Explorer 9 on Windows 7 may have stopped working.