I had this problem once: turned out the alternator field was remaining energized when the engine was stopped, caused by a bad voltage reg. How I found the problem: I could recharge the battery, and the car would perform perfectly until I stopped it for a period of time. I charged the battery and did not start the car; while looking for the current drain I accidentally leaned ont he alternator and it was warm, even though the car had not been running.
There's always a reason.