Corrective Action - Main Processor/Cable:
Examine the connector  on the Maincon or MOCON PCB. Make sure it is not damaged.
Examine the cable. Look for signs of damage or stiffness. The connector  has two housings [2,3] for the cable pins.
Measure the resistance on the encoder cable from leg to leg, and from leg to ground. Make sure each measurement results in an open connection.
Make sure the cable is firmly connected at both ends. Reseat both connections. Make sure the cable is installed in the correct connector at the Maincon or MOCON PCB.
Corrective Action - Servo Motor Encoder:
Check the encoder steps/revolution in the configuration file. Jog the axis and based on the distance the ball screw travels per revolution (ball screw pitch), verify the encoder counts are accurate per each rotation. View the diagnostic>axis page as you jog the axis. The raw encoder count will show you how many encoder steps have been counted. The z axis channel will also show how many steps have been counted, but will reset each time the z-pulse is passed. The z-pulse is the encoder zero point, so it will reset every time the encoder does one revolution. Based on this information, you will know if the encoder works if the correct amount of steps per revolution are counted each time you jog the axis the distance of the ball screw pitch length. If the numbers do not match up, you have a problem.