I'm with Tim, the symptoms indicate that one channel is out of polarity. If the wiring of both output connectors is the same, then suspicion falls on your cables.
Also, I wouldn't read too much into the colors of the wires on the line ins versus the mic ins. Although some manufacturers used Pin 3 Hot for their line ins and outs, the convention on microphones was pin 2 hot since the introduction of the XLR connector. So some pieces, including everything Ampex ever made, was pin 3 on the line ins, and pin 2 on the mic ins.