What do you mean it got the levels pretty close? What levels (+ or - what dB setting?) did YPAO set and what did you change them to? Same for sub level set first time around. Usually YPAO can do well enough, sub level down 20dB is a lot, so I'd suspect something in the way you ran it or even possible something wrong with the mic or what you did to measure. When you manually changed levels you ran tones built into the avr or? Are your two subs equidistant to your listening position? Gain on the sub is set to about half on each sub?