My boss's computer is having the same problem. She has updated to Adobe Reader 9.3.1 and since then has not been able to open any PDFs - I deleted it and reinstalled it, but no luck.
She's running Vista.
wanted to add - i've updated on an XP laptop and am not having problems.
Uninstall Reader, Run the Microsoft Installer Cleanup tool, then re-install.
Problem seems to be solved. I removed Acrobat.com and Adobe AIR using the uninstall utility in the Control Panel. There was no icon to remove the actual Adobe Reader program...not sure why. I then reinstalled Adobe Reader 9 from Adobe.com and was instructed to disable the pop-up blocker on my tool bar. After doing that, the program installed and I was able to open all of my pdf files both in IE7 and from my hard drive. Thanks.