Industrial 3-phase.wiring
Fix your Grounding Electrode System or Neutral-Ground Bond

You need to have ground rods or a tie to an UFER ground set in your concrete.  From there you should have copper wires (typically bare) to your panel. It's not unheard of for those to be stolen.  

From your main panel chassis you should have a bond connecting ground to neutral.  Remember that the first panel fed by a transformer's output is a main panel! This is easy to overlook.  

Also easy to overlook in commercial work is grounding generally, since the metal conduit does all of that for you.  You don't need to worry about it on branch circuits, but it makes the neutral-ground bond easy to overlook.