I think I have it working a bit better now. I reset the settings in H9 Control and stopped trying to send midi via the dins at the same time seems to have fixed the issue. Its a pity you can't control the pedal via the app whilst syncing to midi clock. Or is there a way to do this?

Do you connect to your pedal via MIDI dins or USB? If you use USB, MIDI dins will be ignored and I think you can still use USB to sync MIDI clock while using H9 Control.