Just got my 6040 cnc. Naturally the controller was junk. Replaced the drivers and control card. Everything is up and running, still need to wire the vfd to the controller as well as the E-stop.  My only issue at the moment is the z-axis is stuck in radius.  Any help will be greatly appreciated.

z-axis is stuck in radius

Mill or lathe?

RICH

Mill

Stuck in radius relative to what?

RICH

When I program to a positive 2.0 it goes to 1.0 away. When I'm milling a hole it cuts the hole to size but only goes half the depth I tell it. So if I program it .25 deep it only goes .125 deep. If I program it to Z0. It does go to 0.

Does doubling your steps per unit solve the problem?

We haven't tried that yet. Would ball screw pitch compensation have anything to do with it? If so does Mach3 have a pitch compensation setting?
http://www.linearmotiontips.com/common-ball-screw-terms-explained/

This has absolutely NOTHING to do with 'radius'. The concept is meaningless here.
You need to calibrate your Z axis. You probably need to HALVE the number of steps/mm.

Cheers
Roger