The gains are driven by a low power source input, so by using your bass knob, that could be causing the overdrive as it will take no more than a mm of gain to notice an audible difference when you increase the sensitivity from low input to a much higher input, which is what your bass knob is doing. I recommend not using that at all. If you use multiple gains on a single output, all but one can be down to get the same output for your voltage match. Using more than one gain will cause a huge increase in sensitivity and can cause inaudible clipping even when the gains are only used a bit. Recommend using only one gain for impedance and voltage matching and letting any other active gains set at minimum for a "passive" approach.