It’s likely that the midrange in your tower’s is intentislly Wired out of phase (for better time coincidence). Just skip the warning.
Some Audyssey tips:
1) The first mic position should be dead-center in the seating area, even if you have an even amount of seats (no center seat). All other positions should be no more than 3ft away, do not go around to the other seats in the living room, and it’s ok to have then at different heights (to simulate where your head will be at, such as sitting up and slouching).
2) Dynamic EQ is awesome, but has limitations. It’s default offset, 0dB, is for movies, since tv and music is more dynamically compressed, choose the most appropriate setting for you (I use 5dB as I watch a lot of movies and music that has a RMS-to-Peak dynamic range of like 6dB, so not that dynamic). All this does is alter the frequency response were on listening volume, as our hearing is not linear, look up the Equal Loudness Contours or the Fletcher Munson curves.
3) Dynamic Volume should be turned off, it’s just dynamic range compression (night mode). So only really helpful if you live in an apartment or want use your system without waking up the house.