I assume you discovered the dead battery by turning the key ON and it not starting. When you turned the key ON, the PCM tried to do some initial checks, but with the low voltage, the data collected was corrupted. When you jumped it, it had to collect that data from scratch. You essentially cleared the adaptives and temporary variables when you shorted the leads forcing the PCM to start from the base tables. This is a trick used by some of the extreme fuel economy guys where the ECU figures out what they're doing and compensates over time. Clearing the adaptives at every Start keeps the MPG higher. BTW, this doesn't do much on a stock vehicle.