I'm posting this mainly to provide information for others. I don't really expect someone to provide me with a magic bullet, but who knows.

The guitar level should be completely attenuated when the master volume of the clean channel is fully counter clock-wise and the clean channel is selected. I've noticed recently that sometimes this level control does not completely turn the signal off when the level is fully off. This behavior doesn't seem to be affected by any of the other controls. That is, the pre-amp gain, boost mode, crunch and brightness switches don't seem to have any impact one way or another on the behavior. The over drive channel seems to always work normally.

The problem with the pot was found to be due to a dirty connection in the header on the preamp board. The ground connection of the master pot on the clean channel is provided only through the cable.