First post, but I've had many an AV receiver and can say that I've never really understood why Audyssey gets so much praise. It's not bad, not like the Onkyo AccuEQ system, but I've always had much better success with MCACC.
Audyssey seems, as you have found out, to apply an unnatural veneer to the high frequencies making music far from enjoyable and a little 'hollow' sounding. Audyssey also seems to like setting the sub too low and I've found that its almost like Audyssey wants Dynamic EQ to be engaged at all times to help matters. However, that mode makes the rears seem too 'hot.' Adding 6db to the sub (a Velodyne SPL1200) trim brought things back in line but theres no way of fixing the higher frequencies, unlike MCACC and YPAO.
Basically, I don't like Audyssey and, when I had my Marantz 7010 and a Denon 6200 on home dem, preferred the sound with Audyssey off.