My dealer updated my car in Nov when I brought it in for its 15k service without any problem and I have done the retrofit. Could it be the problems you're having is because you're doing a semi DIY upgrade yourself vs. having the dealer do it themselves? My service advisor said they updated everything to the latest software and although the computer took a little longer and they had to reset some things no other problems. So maybe that may be the problem as I guess sometimes service advisors and managers can be "particular" in what they will do for customer's car sometimes especially when they have done upgrades or DIY work.
Anyway my car runs fine...so far...fingers crossed!
Good luck!