I think you're referring to the music (score) relative to the rest of the soundtrack (dialogue and sound effects) being too quiet? There's no way Audyssey can be responsible for that, unless there's something seriously wonky with the results. It's also possible you have some other feature (Dynamic Volume, Dynamic EQ) that is causing what you're describing.
I would first verify that Audyssey is indeed the culprit by going through the settings and making sure everything except subwoofer crossover (assuming you're using one) and Audyssey correction (no other Audyssey features) is off. Then go through the movie(s) you are having an issue with and see if the issue is still present. If so, disable Audyssey and check again.