Is the battery shorting internally? A stock alternator is only 37 AMP. To burn them up somthing needs to be putting a large draw on them for a long time.
What are the voltages at idle, at 1200 RPM. Also what is the voltage at the alternator VS the battery. Then check the voltage after running for 7 minutes. The voltage should come up. As the amp draw goes down the voltage comes up. And vise versa.