Now if I have a user preset list set up for a particular set, my footswitches don't appear to work…. Is this normal behaviour? I'd have thought that if I have a preset list and was playing from it that the aux footswitch would allow me to navigate up and down as it does on the H9 itself….
I'm not sure I understand. You have a user preset list in H9 Control, and if you're looking at that preset list in H9 Control, you were hoping that the aux switch would step you through that preset list?
You would need to save the user preset list onto the H9 to be able to step through it with the aux switches. You can do that in the Preset List screen with the "Save to Pedal" button.