In other words, if I move the Input Gain slider in H9 Control, I see the same value updated in [UTILS] in the pedal's System Mode, i.e. I read IN +5.5. on the pedal and +5.5 in the Control app. But these values don't change when the MIDI controller changes the volume, even though the HOTKNOB lights change and I hear the volumes adjust. Can someone please explain why this might be happening?
The input gain from UTILS in System Mode is different than the input gain that's MIDI controllable. The input gain in System Mode is gain that can be applied before the ADC converter to boost the signal a bit if needed to improve the conversion quality. That gain is limited to only 12dB and it's cancelled out on the output with a corresponding cut so that there's zero net change in gain.
