Yes, the H9 works fine when I connect just the pre or just the post side. But the noise consistently happens when I connect both sides of the H9 regardless of what cords, stompbox, and power supply I use in the loop. The noise always goes away once I take the second instance of H9 out of the chain.
I'm a bit confused. What do you mean by connecting both sides of the H9? If you connect both sides of the H9 (like what I suggested in my first reply. What I meant was using a cord connecting H9's OUTPUT 1 and INPUT 2 as a "pedal in bypass") it does make noise?
By toggling Pre/Post I meant toggling that in H9 Control's preset screen, with connected cables unchanged. Please find the attachment. You may also do that on your phone.
By doing so you may find out which i/o ports have problems.