The best thing you could do is to put back in the original CPU. Just to see if the issue is caused by ModyPoly or by something else in the Polysix.
In case you do not have that anymore:
Which D# plays the chord? That might help
The only other thing you could try at this point is to try and remove the HiRes board.
this way we could at least check if the issue is caused by it, or by the rest of the ModyPoly circuit.