If you are 100% that your wires are hooked up with the right polarity and your reciever is telling you that they are out of phase, I would assume the issue is with room acoustics and that may be the same reason your speakers sound better when it says they are out of phase. Room acoustics will play a huge role in how the system sounds...if your YPAO is detecting them out of phase when you are sure they are wired in phase that probably means there are cancellations at certain frequencies that the YPAO test tones are due to the shape of the room and/or speaker placement. I don't disagree that the speakers sound better to you when crosswired but I believe with proper placement and calibration(assuming the speaker's aren't crosswired inside) they will sound more correct when they are in phase with each other, otherwise you are creating cancellations at all frequencies, which I don't think is desirable in any way. Like I said before, there are cd's with test's that will help you with the phase of your speakers...the one I have used in the past is on a lense cleaning cd and it was very easy to tell when the guy's voice was in phase and out of phase. Also, be sure that both speakers are the same distance from the listening position. Because of the properties of sound waves(actually all types of waves), when the sound from the two speakers reaches the listening position at different times there will also be cancellations.