Linear Actuator Position Control Reed Sensor

The last two conditionals in loop() are still inside the Serial.available()
test, so they will never be noticed except if a character comes in off the
Serial port.

You need to move them up a level so they always get tested round loop()

@MarkT,
Are these the two IF statements you were referring to :

		if (Extending == true && CurrentPosition > goalPosition )
        	   {    
   	 	   //we have reached our goal, shut the relays off
   	 	   actuatorStop();
  	 	   boolean Extending = false;
          	  Serial.println("IDLE");  
          	   }
  
 		if (Retracting == true && CurrentPosition < goalPosition)
        	   {
        	     //we have reached our goal, shut the relay off
  	 	    actuatorStop();
   	 	    boolean Retracting = false;
   	 	    Serial.println("DELI");  
         	   }