could be the intake valves were off quite a bit so the computer was compensating for it. now, its still trying ot do it. our ecu's take a few starts to re-learn stuff...sometimes it wont throw codes, but it can make a difference in running. i know with older FI toyotas, if your battery dies, you have to run the car and drive it for like 10 min or it will keep stalling the same way b/c its re-learning the air/fuel mix in relation to the older engine!