Ok, so the final update, looks like they got the new software and it's all good to go. BMW was giving me $500 for the trouble, but the Service Mgr remembered me asking about a price on the M Performance Exhaust.... well, he told me they are giving it to me, installed, for FREE because of the inconvenience!! I also purchased the Black grills and they will install those for me too. WOW!
So, 6 days without the car, but a heck of nice compensation on the part of my dealer and BMW!