Here is some more information.
First off, I quoted semitones in the previous post, those were actually cents. Learning all the time.
The behavior changes between channels. Channel 5 is more consistent than channel 6, but it also tends to go sharp on the high notes and flat on the low notes (although that didn't seem to be the case before we swapped the oscillators with channel 6, see below, but again things are ... confusing since we don't know what the proper behavior is. Channel six is off by as much as 21 cent on the low end, where as channel 5 is typically only 8 or so.
We swapped the switches and it didn't seem to make a difference. We swapped the op amps, and it didn't seem to make a difference. We swapped the oscillators and there was a change, even after calibration, but the behavior is still pretty much the same although channel 5 may have gotten worse... It's hard to tell...
I'm tempted to try putting in new caps on the op-amp feed circuit since I have the right kind, but there are eight and pulling the board for no reason seems at best reckless.
While I'm still here, is there anything else we can try?
I'm going to read the previous posts and look at the ADC circuit.
Thanks again for the help.