Okay, but that still sounds like the alternator output current is still flowing through the bulk head connector pins. As Del mentioned the ammeter can be issue but the bulk head pins and original gauge of wire used will always be a potential disaster waiting to happen with a big alternator. Just tying the ammeter connections together isn't enough.
To the original poster- The connector that plugs into the voltage regulator have been known to go bad and cause intermittent connections. Standard Motor Products and Dorman make replacement connectors with pigtail wires. Standard Motor-S573 and Dorman 85126.