I've got this same issue with the unit. If I want to use it for the compressor/OD pedals into the front of an amp it adds a decent bit of background noise that I can't get rid of. And this is just by default of plugging into the unit, without any effects on. This is not an issue with my traditional pedalboard of stompboxes, no noise is added from them but the Helix gives some headaches.
Send outs - If I use this instead of the main out to the input of my amp (set at instrument level) we get a considerable amount of noise even with an empty preset and the out set to the 1/4 (so send isn't even outputing) it's making noise, it's unusable for this purpose. This is annoying because the send is putting out the right level without me having to mess with the volume knob on the unit, but it's unusable due to the added noise.
1/4 main out - If I use this at instrument level I get a lot less noise than the Send (even at line level this is less noise than send) but still considerably more noise than just plugging into the amp, noise that my normal pedalboard does not add. What's worse is that this output is connected to the volume knob, which means I'm now playing guessing games as to where to set it, it never sounds the same as just plugging into the amp.. Again not a problem with normal pedalboard, and if there is a solution to that particular issue I haven't found it.
Until now I've only been using the unit for modelling, straight through to a PA system and it has been fine. This is the first time I've used the unit into an overdriven amp with the intention of using it for boost.
Edit : To add more detail : Amp was a Cornford Hellcat (35w 4x EL84, 2x12).
Helix connected to PC via USB at the same time.
Guitar > Helix > Helix 1/4 out > Amp input = Lots of noise, more noise than when not connected to USB.
Guitar > Helix > Helix 1/4 out > Amp return = No added noise, or insignificant enough to not matter.
Guitar > Helix > Helix Send > Amp return = More noise than 1/4 out, additional low frequency hum, disappears when USB is disconnected and is then equal to the 1/4.
Edit 2 : Helix was not plugged into USB for these tests - Added a 2nd amp = Peavey 5150 into a Marshall 4x12.
Amp 2 : (5150) - Guitar > Helix > 1/4 out > Amp return = Very audible thick low level hum. Seems more to do with the amps FX loop itself, so I will give the Helix a pass on this.
Amp 2 : (5150) - Guitar > Helix > 1/4 out > Amp input = Same issues as amp 1 but worse, noisy.
Edit : Added a 3rd amp, Marshall AVT150 (1x12 hybrid combo, solid state power amp)
Amp 3 : Helix 1/4 out into Return = Same as Hellcat, no or insignificant noise added.
Amp 3 : Helix 1/4 out into amp input = Some noise added, marginally less than the Hellcat but a clear to hear hiss.