cc#1 controls the wah effect. To switch an effect on or off over MID you need to send the appropriate control change command for the slot that the effect is placed in. You can find a complete list of these CC messages in the MIDI chapter of the reference manual on page 388.
Resolved.
I did the assumption that “bypass at stop” would turn off the efx block, but it turns of the wah with the block still active.
2nd wrong assumption: cc would effect the “ manual” parameter…Didn’t have a guitar connected, so didn’t spot all was ok