The original question was never answered. I have the same problem being an owner of Acrobat 9 Pro Extended. The solution presented only addresses Acrobat X and the E Learning suites.
I cannot use Adobe Presenter due to the Internet Explorer 9 incompatability issue.
Sorry if my implied meaning didn't come through in my first post. I tried it and it does not work. Running the Presenter installer on the Acrobat 9 Pro Extended disc merely results in a "Presenter already installed" error. If you were able to get it to work, I'm all ears
I want to mention that Adobe Presenter 7.0.7 work fine with IE9.
Acrobat 9 might behave bit differently. Please try following steps:-
Presenter installer will sniff the system for a valid Acrobat 9 Pro Extended license and will automatically get activated