Mark, it sounds like 39 is "max" as far as the machine is concerned.
I don't see why changing file types would have anything to do with where the volume 'knob' maxes out though. As far as I can tell, the only hint I see is the PCM setting changing is what's messing it up. Quite possibly its requiring a restart of the system after changes, which would answer the part about when and why the changes being made are actually being carried out.
Bob