What if it´s not exactly a PWM problem? Doesn´t it sound like two voices an octave apart instead? In such a case the probable culprit(s), could be the 4052 ICs, ic10, ic2 and ic6. But it´s a longshot. I´m actually clueless now.
About Poly1: when a key is pressed, it will be assigned to one voice, and always the same voice as long as no more than 6 keys are played and the polyphony isn´t exausted.
Ex: Press A3 - keep pressing or lift the key and play repeatedly , doesn´t matter - voice 1 will sound.
press B3 - voice 2 will sound.
press A3 - voice 1 will sound again.
press c3 -voice 3
press d3 voice 4
e3 voice 5
f3 voice 6
now press G3 - voice 1 will sound.
Press B3 - voice 2 will sound.
Press A3 - voice 3 will sound. Because G3 is now linked to voice 1.
Poly 2 is different:
Play any single key -voice 1 will always sound.
Play two keys at the same time -voice 1 and 2 will sound.
play thre keys, voices 1, 2 and 3
And so on.
Playing staccato always the same key under Play2, if the issue does affect all the voices, then voice 1 will be affected sooner or later, and pobably every six times...