Are you still using the Yamaha amp & if so try re-running the calibration settigs again.. I have had a yamaha before the present Amp & to be honest once you have checked all wires & if given the option of ignore the out of phase bit on the amp & you are sure all wires are correct i would ignore it.
This can sometimes happen using different lengths of wire & different types of the same makers wire for example: QED Original for the front L/R &C & then using QED Silver Micro for the surrounds .. this can be caused by a very slightly different resistance, even though wired correctly.. always check they are wired correctly before deciding to ignore the Amp.
I have had a similar problem with my Pioneer amp saying exactly the same as yours, so i re-ran the calibration & it said thay were fine, all mine have exactly the same speaker cable to all 7 speakers.
Regards..