I'd hit up the Audyssey FAQ and go from there. The only thing I can see right off the bat is that you set the internal sub crossover @80. You'll want to turn this off if you can, or all the way up and use your AVR to set the sub crossover, which should actually be at 120. Also, as you are running the calibration, turn the sub to on, then you can turn it back to auto once it's done. Also, the AVR will most always set your speakers to large if they are full range speakers, you'll just want to switch that in the AVR and set the crossovers how you want, I'd start with 80 all around and go from there.