I have a Shapeoko 3 XL. When I initialize at startup the Z moves down by approx 1.5" then errors. It never even tries to home X or Y. The limit switch is at the top so the head moving down makes no sense to me. When I manually move everything into the home positions there are 3 green lights on the board.
This is a new machine to me so fresh install of all software.
The beltZ and HDZ run the same direction. The Z-Plus runs in the opposite direction. On SO3/4 if the Z goes down instead of up you likely picked the wrong Z.