we have alot of Mazak machine tools that are set up in the same manner we have never had the problem you are having but we allways power down at the controler then shut down the transformer. not sure if your problem lies in the transformer or a controler glitch. even if your guy powers the system down at the transformer when he powers back up he still should have to turn on at the controler. so it would be no different than when we have a power outage and our systems shut down and we have no problems what has the manufacture of the cnc said. what type of controlers are on the cnc and what type of cnc is it?