Thanks again for your help Hood and Chaoticone. Let me give you the whole story here as well as what I am using.
When I posted this thread, I was running MACH3 Version R1.84.002, which is what came with the controller when I bought it. I have not used this for a while and here recently I installed 3 Home switches. One for the "X axis ", One for the "Y axis" and One for the "Z axis". I got everything wired up and configured in the inputs section of the Pins & Ports configuration and in the Home / Limit configuration. At this point everything worked just fine except for the Homing order. It would start out with homing the "Z axis" and when it hit the Home switch, it then reversed direction until it came off of the switch. It then did the same for the "Y & X Axis".
I then posted the thread and both responses were directing me to the Operator menu in Mach3 and then Edit Button scripts for the RefAll button. Because this option is not in the R1.84.002 version, I downloaded the latest version of Mach3, Version R3.043.066, and installed it. I made all the config changes and changed the homing order. And this is when the new issue popped up. The Homing order is what I prefer, "Z, X, Y", but now when each of the 3 Axis hit the Home switches, they trip the switch, LED turns Green and the next axis starts homing without the previous axis not backing off of the switch.
Is this normal? How do I fix it so the back off of the switches?
I am running the following:
Controller:
CNC Stepper System by Camtronics, Inc.
Stepper Motors:
MCG
2phase 1.8 step motor
1.3A, 0.5 Ohms, 18.61 W
Thanks for everyones help.