Hi Jared,
I think you probably have more than just your 3 axes defined (which is the default) and one of those axis is disabled.
Assuming your X,Y,Z axis are axis channels 0,1,2 you need to execute a C program to define them with a line such as:
DefineCoordSystem(0,1,2,-1);
After you have all your axes working create a C program that will configure all the parameters, enable your axes, and define the coordinate system.
See Step 4 here (regardless if you are using Mach3 or KMotionCNC):
Regards
TK