Not really an answer to your problem but you shouldnt use the stop button unless in an emergency, what you are meant to do is use the feedhold. If you use the stop button there is a chance that your axis will lose position as the momemtum of the motor/axis will carry on for a bit after Mach has been halted. How much will depend on many factors such as axis weight etc. When you use Feed Hold Mach controls the stop and your position will be correct.
Try using Feed Hold instead of the stop and see if you still get the problem.
Hood