I don't know your wire EDM machine but your problem can be all CNC machines problem if you have ball screw backlash on your X axis. This can be critical if your machine use rotary shaft encoder or stepper motors.
You can use a dial gauge mounted to your machine table and step jog on X in (+) and (-) direction to measure your X axis backlash.
another source of this error can be step loss of your motor drive . if possible swap your X and Y motor drives and test the machine.