Do you have a copy of all of the schematics for the unit, including the control unit and the motor control boards we could look at?
I looked in the forum for the schematics but the link was missing.
Are the 3 pairs of 100VAC transformer windings separate? If you disconnect the transformer is there any connection between the 3 sets of windings? I assume these should all be isolated from each others, both when disconnected and also when the motors are connected.
Mark