I had that problem when I replaced the 30 year old Marchal/SEV/Motorola alternator on my PV's engine with a new higher capacity (55 amp) rebuilt one. The previous one had only one output terminal, the new one had two. Initially I hooked up just one and had odd things happen. I think it was regulating the required 14 volts on the unused output, and as a result the circuit spullying current to the car woulnd't do much under a load. After a fair amount of running it and checking various terminals with a multimeter I finally decided to bridge the two outputs with heavy wire, and it has worked wonderfully ever since.

The wiring is a bit vague on mine, as my car started out originally with a generator, and the previous owner had reworked it to use some huge Chrysler alternator (that very noticably pulsed the lights at low speeds). Then I put in the B20 and Marchal alternator, reusing the existing wiring in a different configuration.