I used to have a 2003 SE CVT (now have i-Shift, worse luck..) Anyway, I always used to find that first thing in the morning it would take several seconds for anything to happen after I selected D or R. I put this down to the fluid being cold, and all the fluid having drained out of the various operating circuits overnight. In other words, it took several seconds for the cold fluid to refill the system before the drive would be taken up. I assumed this was normal; it always did it, before and after I replaced the fluid as part of the regular servicing routine. I also changed the battery on the car and it had no effect on the CVT so I don't think your flat battery is a factor. I've never heard of anything needing to be 'recalibrated' on the CVT. Try just waiting a few seconds when you select D or R first thing in the morning, to give the fluid a chance to get round.