Ensure Feedback in Setup

To verify the system is communicating with the controller properly:

Depress the Emergency-Stop switch
Start the CNC interface
If there are warnings you are attempting to work around, dismiss them.
Click Setup
Click Diagnostics
Push the machine in all possible axes and verify feedback on the axes in diagnostics as per the image below. For the Z axis, if it is not dangerous, depress the Brake switch momentarily, which will cause the axis to drop and provide feedback.

If all connected axes show proper and consistent feedback, then the connection is likely good. If only some axes provide feedback:
The cable between the PC and the Controller box may be damaged
An encoder on the motor may be damaged
A motor signal cable may be damaged
A circuit board may be damaged.