I wouldn't get too worked up about some of the 'out-of-phase' readings for the 'wiring' option when running the YPAO Auto Setup feature. If you've wired your speakers correctly, this step isn't needed and from my own experience on my RX-V2500, I suggest skipping it. The speaker size test doesn't always yield the proper results as well.
Having said that, the distance, equalizing and level setting options have almost always worked fairly accuratey when testing against other equipment (SPL Meter, Room EQ Wizard, etc.), so while it does a decent job with some of these functions, I wouldn't necessarily say its the 'end all, be all' solution for receiver settings and calibration.
On the whole I'd say Denon's Audyssey MultEqXT works a bit better than YPAO, but they both have their own quirks. I suggest using them with an SPL meter for more accurate results. -TD