My apologies to the OP for borrowing this thread.....
I agree that Audyssey, or any EQ, system cannot tell what is causing any detected frequency response problems; that is what the listener needs figure out early in the setup process. Unfortunately, this is very difficult to do for the great majority of HT users.
That said, I believe that the majority of the problems most users encounter are in the low bass area (that sure is what is asked about the most on the HT Boards). Room acoustics, speaker capabilities and placement (especially the subwoofer), are all big players here. Before any EQ is applied it is always best to optimize the system to correct these possible problems to the extent that is possible based on a user's specific equipment and room restrictions. Once this is finished then Audyssey can finish the optimization process to help produce the best bass response that is possible within the restrictions just mentioned.
As you mentioned, Audyssey covers the entire band, however by far, most Audyssey "horsepower/resolution" is reserved for 300Hz and below. I think in most cases (if I remember correctly from Chris' comments over the pass few years), Audyssey has decreasing impact on frequencies as you go up the audio band. My guess is that most typical users would not notice any difference especially if they usually apply one of the post-decoding algorithms (THX, etc.), which all effect the frequency response to some degree or another.
I understand that your experience with Audyssey is different, but your equipment is far better than the great majority of HT systems and I would hazard a guess that you have treated your room also, so any EQ system probably has a negative effect on your system. For the rest of us, Audyssey provides a powerful tool that was never available to us before. Besides, if Audyssey has a negative effect, either real or perceived, then they can always just turn it off.