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Try going to the Pedal tab, MIDI Settings, MIDI Clock, and set Enable MIDI Input Clock to No. It's somewhat counterintuitive. I end up setting it back to Yes (more specifically, CLK IN = ON in the PitchFactor) when leaving H9 Control over USB.
At that point, it's controlled by my system's MIDI Clock over MIDI DIN. Not the easiest method for programming presets with H9 Control, and then re-integrating it back into the context of my working setup.