Had a problem on Mitsubishi machine H-5A. When commanding a tool change the tool was called up and placed above the spindle. However the ATC did not exchange the tools and came up with a YZ not at 2nd reference return alarm. The position in the screen had a #2 next to them so they were in fact at 2nd reference. The machine had a Mitsubishi M3 control on it. On this control someone had changed the Zero return position and 2nd reference position. However there is also a fail safe in the control. to prevent excessive changes and keep the zero return within the factory envelope.