Are you setting up the Kemper to send program changes to the pedal? If so, you must have them connected to the MIDI output of the Kemper. If you want the GT's MIDI commands to reach the pedals, they need to be plugged into the Kemper's MIDI Thru. In a configuration like this, you're better off controlling everything from the GT and not have the GT controlling some things and the Kemper controlling others.