Sometimes phase response of speakers is influenced by the room or by their position in the room - have you tried moving the FR speaker?
Your automatic room equalization probably isn't completing - can you turn this feature off? How does the center sound then? Can you manually set the crossover points for all the speakers or is it only part of the automatic YPAO? If it allows manual configuration of crossover points, select them according to the low frequency response of your speakers and try again. Do you have a sub? More details might help someone with expertise on the Yamaha AVR.
2-Ch (HT L/R): Oppo BDP-105 BD, Adcom GFP-750 pre, Bryston 10B Sub Xover, Bryston 4BSST2 / Paradigm Signature S4 v.2 (L/R), (2) SVS SB12-NSD (Subs)
Home Theater: Bryston 4BSST2 amp / Paradigm CC-590 (C), Outlaw 7700 amp / (4) Def Tech UIW-RSSII (LS/RS/LB/RB), Samsung 46” 3D LCD