Can you use a MIDI interface (or some other piece of gear) to confirm that the MKV is sending what you intend, and to confirm whether the H9 is responding to what it's receiving?
From the sound of it, the MKV should be sending a PC to the H9, followed by a CC to the controller mapped to the EXP pedal. Do those things happen correctly in isolation, when you do them by hand? As an option, the H9 responds identically to MIDI over USB as to MIDI over the DIN jacks, so you can debug the controls from a computer. I recommend the program PocketMidi as a bare-bones way to send arbitrary messages.
As a point of interest, do you happen to be controlling your H9 both through the USB and the DIN jacks at once?
