I am running my Helix with a Blackstar Series One 45 using the 4CM and I am not noticing these issues. What I did was create a rhythm channel that is just a send/return to my amp and a noise gate. A very simple patch. I would try something like that and see what you get. Maybe just create a patch with a send/return to your amp and see what it sounds like. I also believe you can set the send/returns to line or instrument level. You might want to test that as well.