So I figured out that when I am switching presets from the blue/red channel preset over to the green channel preset I only get the popping sound if I'm sustaining a chord or a note. In other words, I don't get the popping if I'm not playing at the moment I'm switching presets.
I also setup a single preset that contains separate foot switches in stomp mode to only change the channels (separate switches for green, blue and red). I do not get any popping when switching any of the channels (via midi) in stomp mode regardless of whether I am playing chords/notes or not during the switching.