A quibble: Onkyo AVRs use Audyssey equalization. YPAO equalization is proprietary to Yamaha AVRs.
The principle is the same, however, and I have the same suspicion as to the cause. The AVR simply does not have enough power to drive those speakers in your room when their sound levels have been calibrated. You might consider replacing the surround speakers with more sensitive ones.
Marantz SR7009 avr + MM9000 amp --> Atmos 7.1.4
Fronts=NHT 2.9+AC2, FH+TM=DefTech PM1000, LCR+TM amped