I agree that the transmission adaptations can make a difference, but assume for a moment that there is no problem, only the adaptations have changed. If he liked the shifting characteristics before the service, and not after, then it is most likely that the adaptations were reset during the reprogramming. That is to say, that resetting it again will move it further away from where he wants it (with learned characteristics matching where it was before the reprogramming).

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2007 X3 3.0si, 6 MT, Premium, White

Retired:
2008 535i, 6 MT, M Sport, Premium, Space Grey
2003 X5 3.0 Steptronic, Premium, Titanium Silver
2002 325xi 5 MT, Steel Grey
2004 Z4 3.0 Premium, Sport, SMG, Maldives Blue