There are a number of things that could be causing this, but the number one
thing is usually 32bit/64 compatibility.
Can you double check if the App Pool is in 32bit or 64bit mode, I had a
similar issue when installing CF9.01 onto a Plesk Panel system and found
that the App Pool needs IIS6
Well if CF is working and .net isn't this could be considered OT ;)
Have you tried any of the solutions found on the web?
http://stackoverflow.com/questions/2654514/getting-the-webresource-axd-handler-must-be-registered-in-the-configuration-to-p
