The system might be detecting a phase issue with the sub’s crossover that is doing bad things to frequency response in the crossover region, and is increasing the mains distance to compensate. Try reversing the phase switch on the sub, if there is one and see if that makes a difference. It would require measurement software and mic to see (graph) exactly what is happening, both with YPAO’s recommendations and your manual adjustments.
Regards,
Wayne A. Pflughaupt