I don't have the same amp that you have but I have experienced the same sort of thing with my tube preamp. I have two chanells and a stacking function that is controlled by two front channel switches which are over ridden by the foot switch.
Sometimes, out of the blue, when the amp is in stacked mode (both channels on in series) it would appear to switch to the clean channel, but there will be no sound. Making any sort of channel selection would give me sound again.
My issue turned out to be an 'ambiguous state' in the switching circuit that exists only when the front pannel switches are in a certain configuration (clean channel on and stack on) and I am using the footswitch. If I change the front pannel switches to any other state, the problem does not occur.
I'll take a wild guess and say that maybe you have a voltage drop in your channel switching circuit (or a floating ground) when you adjust your tone control, possibly caused by a crack in the pc board or faulty connection?
That's purely a stab in the dark, I know nothing at all about your amp.