Thetech: It seems your advice is most unuseful here. Telling someone to go back to their dealer and say "You need to prove it was the aftermarket stuff otherwise you need to keep working on the car" Its just basic social skills and dealing with people that should really tell you that this approach will get him nowhere. You catch more bee's with honey is a saying that comes to mind. Even if you speak the truth, the delivery of information is suspect.
Personally I would have (too late now if you took the other approach OP) was went and said : Hey, I really really appreciate you guys taking the time to look into this when it very well could have been the other installer's mistake. I am going to go talk to the other people and get a list of what was done exactly for their install and bring it back to you. I am happy to pay for diagnostics out of pocket and repairs if you guys are sure it was their fault, no problem at all. I just appreciate you taking care of this and I would like to put a good word in for how helpful you have been and how out of your way you went to help with your manager. Let me know if you want me to pay out of pocket before hand or just bill me.
9 times out of 10 this will have had them continue to work on his car and do it willingingly and happily. Probably would go the extra step and do it even more quickly. Empowering someone to want to do it for you rather than strongarming is a lesson 99 percent of people need to learn.
Sure 1/10 dealers may demand money upfront, refuse the repair etc. However that puts you on par with the 9/10 dealers who would refuse working on it if you strongarm them.
Just my .02
In the end, when your installing electronics on modern cars its an entire crapshoot if you need to access the ecu which is essentially everything. The install on an m3 with an entirely different ECU is different on your past 335 and every other model year of bmw. I have no doubt it was the installer. If it was not than do as everyone is saying and get documentation.