FWIW, I have seen Audyssey set the levels for rear speaker far too high when I helped a relative solve a similar problem. Determined to find out why, I asked him to show me exactly how he had done the calibration, step by step.
We went through the front three, and when we got to the rears the cause became clear to me. He was holding the microphone in hand, and it was in front of his body as he sat in the MLP. I suggested he start over, but this time make sure the microphone is held at ear level for each reading, with nothing around it. Essentially, hold it up and get your head out of the way.
All better. Only a couple of minor tweaks to levels after calibration to fine tune it and it's great.