This is caused by a conflict between the global MIDI channel and the Part 1 MIDI channel. See the help pdf "a guide to using the Supernova II Multitimbrally with a sequencer".
The guide can be found on the Supernova 2 downloads page.
The Supernova II changes from Performance to Program modes when a Program is assigned to Part 1 of the Multitimbral Performance template.
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