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.


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I first tried the backlash test, and all was good. THEN I used G81 X and Y (didn´t use it for some weeks) and made 1 square and 2 holes , all ok... Do you think that G81 was vital ??