I have a Warmoth Mahogany Strat with Dimarzio Super 3 in bridge and Super 2 in Neck. Straight in to Helix, I haven't checked the input settings so I don't know if pad is on or not, I use the main mono 1/4 output directly to the EVH 5150 III Effects loop Return.
However I think its worth noting that this issue occurred with Very low output PAFs in a Les paul and going into a PRS archon 25 combo effects loop return as well. For whatever thats worth.