I'm having a very similar problem that just cropped up on a 6 year old MKII Shortboard. I'm not sure they're the same issue, though. In your case, have you checked the pedal calibration? If you've never done that, power the amp off and hold down the "D" switch when you power back up. It will walk you through a process to set the pedal volume from 0 to 127. Push all the way down with your toe, press D, pull it all the way back with your heel, press D again, it will have you push the Wah switch, press D, and then it will give you a calibration check.
My problem, which just cropped up, appears to be that the expression part pedal is no longer being "detected" by the unit. When I power up I can only get volume in the Wah position, but I have no wah control. Also, I can't walk through the calibration process. It gives me the tow down message, I do and press D, and nothing happens. I'm kind of thinking I'm screwed on this one and have to by another shortboard, but maybe not. Any help on this would be appreciated.