If the machine knows the wires are backwards, there almost has to be a short to ground somewhere.
The machine applies 12 volts to the field on one wire and grounds the other. If there was a short, the logic in the tester would see that short and assume the person hooking it up did it wrong. When he reverses it, the shorted field connection is now hooked to the machines ground. The logic now sees a complete circuit with a good ground and less current draw on the 12V feed. Machine is happy, the alternator tests good. Unfortunately, because of the internal short, it will not work right in the car going to full output at all times. Powerquest is right, the alternator is bad and as I suspected, the parts store testers do not fully test dual field alternators.