Hmmm. Did you disconnect the battery lead from the alternator and then check each one separately? It seems odd that the charging circuit is the culprit but the lead at the alternator doesn't indicate that. The only time I have ever personally seen something like this was on a 360 where the harness to the alternator had rubbed on the intake manifold and there was an intermittent short to ground. Took a long time to find that one.