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MIDI clock illustrates the problem – if it was getting two different clocks, it is not at all clear what it should do.
I'm seeing what the issue was here – at least with the PitchFactor under H9 Control. With USB connected – and with or without MIDI DIN input connected – I was getting the Clk In -> On flashing warning. A sure sign that the PitchFactor was not receiving MIDI Clock from any source.
Somewhat counterintuitively, System Settings -> MIDI -> Clk In -> OFF (or No in the H9 Control) establishes bi-directional (MIDI Clock) communication between the PF and H9 Control. Under that condition, I've found that the DIN input can stay connected – even with an incoming MIDI Clock – without affecting the link.
That's going to help with compiling a large number of presets that may or may not be sync'ed to tempo.
