AVR room equalization errors

I have an RXA3010 (Yamaha) and when I do the room measurements through it's YPAO mike, it gives me errors on 5 of the 6 speakers being out of phase, and 'finds' a center channel speaker that isn't there (yet). the speakers are in phase, and the mains are run through an outboard stereo amp. This is my first time using anything like this, so I'm sure it's user error. It may just be that YPAO isn't good, but it's what I have.... Help please!