if you only want to switch between an A/B setting of the amp have you tried putting all the matchless changes on a foot switch or do you use settings inbetween?
The reason the wah isn't working with the foot switch is that the button on the expression pedal doesn't turn it on/off, it switches between exp 1/2. So when you hit the regular foot switch it is activating the wah but the parameter is assigned to the wrong exp pedal and your still on the exp pedal that has the amp settings. if that makes any sense
To get around this I would either try to set the A/B foot switch like I mentioned earlier or get a second expression pedal to assign it to.
