I've noticed on mine (which hasn't been reprogrammed at all) that when I pull off the brake, I feel a little shutter or a small lurch (doesn't really make the car move forward, but more or less feels like a small quick "shake") and then i'm going.
Is this what the reprogramming will address?
I've also found that at times, my car will have shifted all the way to 6th gear by the time it hits 40 mph in city driving, which seems a bit odd to me, because I would think it would be in maybe 3rd or 4th gear at 35-40 mph. I'm not a trans tech, so I could be wrong.
It's much better than when I first got the car (car has 6200 miles on it now) but I think it may still need improvement.