Just wanted to share this in case someone is running into similar issues:
I experienced some crackling when listening to audio from my PC connected to my Helix LT with the usb cable. Playing my guitar through the helix did not cause any crackling. So I figured it must be something on my PC or the connection and tried everything (software Update, Buffersize, different cable etc.). Nothing fixed it. I noticed it was only on one preset, which is weird, because why should my effects affect the usb audio? Turns out the preset was pretty DSP heavy (Poly Capo, 2 Amps, Reverbs...). For whatever reason this messes with the audio. Especially setting the Input to "Multi" made it much worse, otherwise it was less noticable.
I have many other Presets which also pretty much max out DSP and are set to Multi Input, but they dont have this problem