You didn't mention how the alternator was wired up. Might look at the Mad Electrical web site. He talks about different ways to wire up an alternator and what happens (similar to what you said) when a one wire hook up is used. Read on his "Tech Tips" section or call him if you have any questions. His name is Mark and he's a really good guy. J.M.O.
Not affiliated with the company other that a very satisfied customer.