Glad to hear it was not a hardware problem, @unbracketed!
I thought having level controls inside the Duo’s webinterface, too. My favourite approach would include these controls in small-ish side-panels right and left to the pedal board design canvas. Just two/three small volume knobs for the hardware gain stages right next to the connectors (instrument I/O + headphones). Visibility of each panel could be toggled with a small icon north west and north east on top of the pedal area.