Let’s check against the description on page 42 of the manual:

If AUTO is chosen the first MIDI channel used by the audio tracks, and not used by any of the MIDI tracks, will be used.

Would that fit the behaviour that you observed?

Using a value of AUTO for the CHANNEL setting in the PROJECT > MIDI > SYNC menu does not mean that you are setting the Program Change channel to have the same value as that for the AUTO channel in the PROJECT > MIDI > CHANNELS menu.

I doubt that you have found a bug, but please confirm.

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