i own the boston VR3 towers. and i have the predecessor to your receiver (mine is the yamaha 2500). i had the same issue when i ran autosetup; it told me the speakers were wired out of phase. i called yamaha about this and they said that with certain speakers, the autosetup might give an erroneous reading. as long as you are certain that you speakers are properly connected (plus to plus and minus to minus), then i would choose to ignore the error from your yamaha's autosetup.