I think it boils down to the fact that you should NOT use "toggle".
For each stop or button do the following:
General settings
Switch MIDI Inputs
Scroll to the item you wish to control
Make sure "toggle" is NOT ticked
engaging (use whatever MIDI message your stop or button sends
disengaging (leave as "automatic")
Organ settings
Connect Switch MIDI inputs to organ switches
Scroll to the item you wish to control
engaged (Change state)
disengaged (none (no effect))
This works for me.