Hopefully the Hauptwerk setting will work for you, but if it doesn't:-
The switch mechanism in toe pistons that are typically found on older church organs consists of a plunger or piston sliding between two strips of springy metal. When used in low voltage MIDI installations these toe pistons generate multiple MIDI messages. The solution outside of Hauptwerk is to fit a magnet to the plunger and a reed switch instead of the springy metal strips.