From the designer of Audyssey, Kris Kariakarkis: -
MultEQ detects absolute phase for each loudspeaker. Some loudspeakers are designed with intentional phase reversals in the drivers in order to address crossover problems. MultEQ will detect that and report an error. The best course of action is to simply check the wiring and press "Skip" if it is correct. MultEQ simply reports a possible wiring reversal, it does not automatically switch the phase.
As I suspected if a speaker has drivers with phase reversal, you get the message you are getting.
I guess you can press skip and Audyssey will accept the error that can not be corrected and proceed.
However, having speakers with phase reversal of drivers in a HT system is a bad thing, unless all speakers are identical.
The phase reversal is necessary to prevent a null at crossover. However out of the crossover region the drivers are out of phase. If you are using a single set of speakers there is no real problem unless you believe in absolute phase. Although I have a feeling this can't be a good thing in a speaker and have sought to avoid it in my designs for a long time.
It is a bad thing when you have different speakers, as if some speakers have phase reversed drivers and some don't, then there is no way the system can be correctly phased and so this will affect overall sound quality in a significantly negative fashion.
Say you have mains with tweeter phase reversal but not the center, then the tweeters will be 180 degrees out of phase above the crossover region. That is a really bad thing for imaging coherence and blending of speakers.
This probably occurs in systems more than people realize.
In your case this confirms my suspicion that some drivers have phase reversal in your system and all drivers are not in phase.
This is reason enough to update your system, as this will limit performance of your system. Unfortunately you can only correct this with a new set of speakers.