Hi,
This is just a guess, but a bad DAC could cause that sort of problem. They tend to fail with one bit stuck either high or low - if a low-order bit has failed then the autotune would probably have enough range to correct it at one particular point, but as soon as you start trying to play different notes it will not track properly.
In my general experience, DACs are one of the less reliable components in vintage equipment, so that is where I would start looking. The easiest way to check is to swap it with the DAC from the other voice board. Another possibility is the two 8-bit latches that deliver digital data to the DAC - checking for activity on all 14 data lines would give you an indication of whether they are working properly.
Or it could be something completely different ;-) But that at least gives you a starting point. Good luck!
Cheers,
Steve L.
Benden Sound Technology