Hi,
it sounds like you have your Z axis set up funny.
Most CNC's are setup so that the very top of the Z travel is machine coordinate zero, ie Z axis Home.
Any real Z axis moves 'within' the machining volume will occur at negative values (Machine Coordinates) of z.
Your Work Coordinates are usually set to zero at the surface of the material, so a cutting move will be negative z but
a positive z will be above the work, note.....Work Coordinates.
Is this how your CNC is setup?
Note that the Safe Z Setup page allow you to choose Machine coordinates, Work coordinates and Incremental.
What have you set? Why did you choose that setting?
Craig