When things get confusing, go back to the basics. The most mysterious problems revolve around the grounds or as I call them, RETURNS because this is the other 1/2 of the complete circuit the ground or return side. Run a heavy gauge jumper from the case of the alternator to the heavy gauge termination of the negative cable from the battery. Don't assume there is a good conduction path from the alternator case (negative side) through the engine back to the negative cable attached to the engine. Then retest the alternator and proceed with troubleshooting if needed.