It's always going to be a trade-off between noise and sustain with a gate. You can lower the threshold, which will keep the gate off for lower guitar signal. You can make the attack longer so the gate takes longer to engage, but that will give you noise if you play staccato. You can also alter the knee. Basically threshold sets the level where the pedal gates. Attack sets how long it takes to gate. Hold sets how long the pedal waits before it checks for signal again. Release sets how fast it opens the gate. Damping sets how much it turns the signal down when the gate is closed. The knee sets how sensitive the gate is near the threshold. Hard knee gates right at the threshold, soft knee gates a like at a time. I believe ratio is related to this. Best bet is to find presets you like and look at the settings.
Ok, so it works the way you want until you disconnect the PC. Seems like you must have it set up right. I wonder if you're storing it correctly, or if the series parallel modes can be altered by a controller or something.