I've compaired two machines that have had this issue. One I fixed by simply reinstalling v9.3.3 off the Adobe Site. Once fixed I compaired the Registry Settings to the one that was still broken. I found that a registry setting was missing in HKEY_CLASSES_ROOT\SOFTWARE\Adobe\Acrobat. All you have to do is right click on Acrobat, select NEW --> KEY, and call it EXE. Select the newly created folder, and in the right pane, right click, select NEW --> STRING VALUE. Double click the newly created string and under the Value Data: copy and paste the following line including the qoutations. "C:\Program Files\Adobe\Reader 9.0\Reader\AcroRd32.exe" Once you are complete, close IE and reopen it and try and open a Adobe Reader File.
If you want the easier method you can also copy and paste the following code into WordPad and just change the file extention to .REG
Then all you have to do is double click the file and it will insert it into the registry automatically.
Windows Registry Editor Version 5.00
@="\"C:\\Program Files\\Adobe\\Reader 9.0\\Reader\\AcroRd32.exe\""
Hope this helps,