Presume your using gerry's screen set.?

Have you set the clearence plane.? and is the number positive not negative.?

With all the issues you have been having with changing axis directions etc could you possible have the Z axis going in wrong direction.? IE down = positive Z axis are nearly always negative moves down with positive up.!

Test by zeroing dro clear of any obstructions and typing G1 Z-5 F100 in the MDI box. This will move nice an slow 5mm down. If goes up your set wrong.!