I have the same issue. I go through and reprogram A, B, C, and D with the channel volume knob vertically centered. The volumes still largely vary. The distortion channels have more output than the clean. So than I have to do it again and again. And standing next to the amp to turn reprogram doesn't help...
So when I crank it up and it's mic'ed at a gig the variables in each channel volume become much more obvious. You almost need a decibal meter to get it right. I believe there's an Android app but I don't know if it's accurate.