Actually, the volume pedal works independently from the master volume and all other output volumes (Reference Manual p. 33), so linking or unlinking shouldn't make a difference, I think...
@CPHfx, how are you connecting your pedal?
You may be right, I'm at work also. One thing to try for sure is isolate it by not using wah for now. Just hook up and only have the pedal work the volume. You also should calibrate the pedal using "Init".