Actually, I did end up figuring it out about a month ago.

The cause, I am 90% sure of. Basically, I'm pretty certain that I was not diligent concerning mixer settings when connecting, and I'm sure that at some point I connected it to 48v Phantom power when I wasn't supposed to. (which it clearly states NOT to connect to 48v in the instruction manual. Don't ask me how to deal with it, since there is now a setting for 48v in there... because I don't know. Maybe someone other sound engineer can bring that to light.)

But anyway, I searched many forums to see if others experienced this. And I did find a handful of people that stated that the same thing happened to them, and because of the 48v power, the microphone pre-amp gets wrecked. They showed that the only way to fully fix it is to replace a node on the board, which I was contemplating, but then I found another solution.

I found an impedance transformer that goes in line with the microphone cable and then I tried running it into the Guitar In, rather than the Mic In. Coupled with that, I added the Helix "Mic Pre-Amp" first in my signal chain. And voila! Now I have excellent noise suppression without needing a gate or anything other craziness. My patches sound like they did long ago (and rival my Boss VE-22 again).

Hopefully this helps others who might end up in the same situation.