May be it's just that it's Monday, but I'm still a little confused.
What is your primary system - 480 delta or 480Y/277?
You say you are measuring a voltage from the "neutral to the equipment ground conductor". By this do you mean from the control transformer "neutral" to the control panel ground? Or do you mean from the control panel neutral to the building ground?
As, I said, my head is a little fuzzy this morning so I don't know if this is going to be valuable. Could I get a couple of more voltage readings? (Grid is your 480 system, CPT is from your control transformer)
480 grid phase A to grid neutral
480 grid phase B to grid neutral
480 grid phase C to grid neutral
480 grid phase A to grid ground
480 grid phase B to grid ground
480 grid phase C to grid ground
480 grid phase A to panel ground
480 grid phase B to panel ground
480 grid phase C to panel ground
480 grid neutral to grid ground
120 panel hot to grid neutral
120 panel hot to grid ground
120 panel neutral to grid ground
120 panel neutral to panel ground
Also what happens when you lift the ground connection from the control transformer.