Thanks for the reply.
It makes the same noise with the foot pedal or with the button on the amp. It also makes the noise whether there is a bass signal or not. In fact, it makes the sound when there is no bass plugged in at all. It is more noticeable at higher volume and is at its worst if I have a note ringing when I switch. If I switch "between notes", it is not as bad but still present.
It is obviously not the instrument cable or foot pedal cable since I can recreate it right at the head by using the button.
I have only tried one cab, an Uber 210, so far so maybe I can try something else tonight. I have a Shuttle 112 extension that I can test.
I have a note into GK so hopefully they can point me in the right direction. Unfortunately I bought the head used from the TB classifieds so there is no warranty for this.
The thing sounds pretty good other than this but I bought it primarily for this option so this is sort of a drag.