Hmmmm, Something sounds weird about the way you are describing your problem. Normally when you "Ref all Home" the first thing that should happen is that your Z axis should move to it's home position, then the Y, then the X. You don't mention what happens with your other axis when you ref all home. How about a little more information about what exactly happens and what your equipment setup is (i.e. how many axis, what kind of motors, drives).
Regards,
Sid