Is this a Wye-Wye transformer? If not, how are you reading primary voltage to ground?
Is this one of your company's products that is under development, or is this an item that is already being marketed?
Has this particular setup been working properly for some time, and is only now showing the problem, or was this set of readings taken as part of a QC test prior to the machine leaving the factory?
I am inclined to think that either there is a defect in the transformer windings or an error in the secondary wiring. (Edit: To correct a spelling error)