I hope it's something simple. Some forums have some very detailed instructions on setting up Audyssey.. maybe you missed something or left it in some compressed mode for night listening, etc, or something else ON, when it should be OFF?
I have no idea, and I am getting mine delivered tomorrow. I have read a couple of complaints like yours but most don't seem to be having any problem.
Make sure your sub pre-setup is correct also.
You can do the ol' meter and tone setup and not do Audyssey. If it works better than at least you will know the AVR is probably ok and it is something in the auto-cal that is causing the problem.