My guess is that with the battery totally dead, the ECU lost all it's memorized settings on the engine and had to re-learn everything from scratch. Same thing happens to the older trucks too if you disconnect the battery or ECU. Nothing unusual or bad, just part of the process inside the computer.
My oil line fix
My 100k stopped odometer fix
Brace for impact, I'm in a "modifying mood". Massive thread count inbound.