I had a similar issue. I can't explain why, but when I put the volume control block at the end of the chain it almost completely disappeared. I use the Helix Floor primarily in stomp mode with snapshots. I haven't used the amp modeling live. My amplifier is a Boogie Mark IV and I use a Voodoo Lab MIDI amp channel switcher to switch between channels on the Boogie. The Helix Floor controls the Voodoo switcher via MIDI. On the Helix when I had the volume pedal block at the start of the effects chain I would get loud pops changing channels on the Boogie. Now that I moved the volume pedal block to the end of the chain it's gone. I hope that helps.
