Can you check if Marbles’ miscalibration is on the input or output side?
Disable the external processing mode. Set STEPS fully CW, SPREAD fully CCW, and turn BIAS. It should generate perfect octaves. In particular, if BIAS is set to its minimum position (with the unipolar output range), the output should be 0.000V and should not cause any detuning when patched into a VCO. If all goes well at this step, then the miscalibration is on the input side, if not the miscalibration is on the output side.
Also, regarding your other question… I haven’t had the time to try on a real module, but I looked at the code and came up with the beginning of an explanation. In short, Marbles has three “output things”. When it’s set to external processing mode, with a common clock, only one “output thing” is active and records the notes. The two other “output things” are slaved to the first one and replay the sequence shifted in time, they don’t see the input signal. If you remove the common clock, these two other “output things” will no longer be slaved to the first one but they haven’t recorded any note because they were slaved, so they are stuck with whatever they were doing before you enabled external processing mode. I think I can come up with a software fix for that.