I have never had any problems with my Shapeoko Pro XXL after 3 years. After not being used for aboutthree months I went to initiae machine and the z axis moved in wrong direction and made grinding type noise until initiation failed and gave message that limit switch was not found.
On an SO3 the HDZ and belt drive run in the opposite direction from a Z-Plus. Not sure about SO4. So run configuration to fix and then see. Usually the Z goes up to home but if it goes down it is usually the wrong Z selected.