Last time I tried, IE9 64-bit, it did not work with the debug version of flashplayer. I saw the same message you have posted. Therefore, I will recommend sticking with IE9 32-bit version. This is what we have been using.
Also, make sure that you have specified IE9 32-bit under TestedApps in your project. Otherwise, if 64-bit is specified, you will get the message you are seeing.
In addition, if you have used notepad to create/edit mm.cfg file, make sure you have not saved it with txt extension. Try saving it by setting the "Save as Type" to "All Files" in notepad.
