This is actually considered part of their charm. Just keep tweaking the knobs (including the volume control for the channel your NOT using) until it sounds good.
I read an artical about Neal Young's rig. His Deluxe is set up with a servo motor pot for stage adjustments on the fly. On the volume control of the channel he's NOT using.
This really is considered a standard way to adjust the tone on these amps from what I've read. In fairness I have never owned one. But if your really upset by it I think Bruce has a recommended mod to make the volume controls more independant. But you may lose some of the available tones with the interactive volume controls.