Which Ultra do you have? My drawings for the Ultra 60 and 120 as well as the Ultra Plus have no transistors in the channel switching.
On other PV AMps like the XXX with xstrs, it would be odd for all those to go. But since PV uses mainly relays, there is not much complexity to the circuit. WHat is wrong with the transistors? Without a FS plugged in, on those PV amps, the transistors turn on and hold the relay circuits active. The pedal grounds the bases of the transistors and they essentially disappear.
Ultra, Cruch, and Clean are not usually three channels to switch between. Usually one switch switches between two - ultra/crunch, for example - then the other switch selects either the clean or those two. So for example, of you were in ultra and hit the clean switch, you'd go to clean. But if you then hit the crunch switch, nothing would happen because you were still in the clean. Now hit the clean switch and it goes back to ultra/crunch, and since you just hit the bitton, you will find yourself in crunch rather than the ultra.
Various of their amps work that way in various combinations. Point being that on some models there are certain channel transitions that will require pushing two buttons. If that is what you are trying to fix, it is wired that way.