I would start by setting the subs manually to the measured distance and see if that clears up the phase cancelation you measured at certain frequencies. I had the same problem with audyssey, sub was 5.5', audyssey set it to 7.7', and I had a huge null at 50hz. I think sometimes automatic room correction may get confused by the out of phase signals coming from the port or room reflections at low frequencies.
Use a tone generator app on your phone or download a file of the frequency that there is a null at, and slowly adjust the distance until it is the loudest, that's what I did and it worked well for me. I'd do the same with the speakers, just set the distance manually. Sometimes in small overly reflective rooms room correction gets distances wrong.
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