You might try a reset of the avr; I'd try a soft reset first, unplugging it for a bit, a factory/microprocessor reset if the soft reset doesn't do it.
Not very familiar with the Yamaha setup but not sure why the position of the avr would matter...or are you putting the YPAO microphone on the avr? On my Denon and Onkyo avrs I can set the sub level at the beginning of the Audyssey routine, the speaker levels are determined separately. I think I've read the sub/speaker levels are more intertwined with YPAO, tho.