CPVO,
see my message 2 post above yours. You will see I had the same problem with my 2010 RT and the BBK 85mm TB. Has to do with the idle speed not returning to setpoint before a predetermined amount of time on start up. When I first installed the TB would happen all the time. Then gradually became less frequent until eventually stopped happening. When I called BBK they gave me a song an dance about how they test the units on Challengers and they are supposedly fully compatible with the OEM electronics. My understanding of the issue is has to do with combination of the CAI and TB changing the fuel/air ratio to a bit lean and the onboard computer cannot initially compensate. Overtime the system "Learns" the new setup and makes the corrections. However, the best way to correct it would be to have the car tuned and adjust the F/A ratios to optimize the performance.
With respect to installing a non-OEM tune, I would suspect the dealers would use this as an excuse to avoid repairing the drive train under the warranty. I have never used the handhelds but I believe you can store the factory tune and reload it if you need to take the car in for service. But if you go to one of the threads covering tuning questions, there are plenty of folks who can answer better than me.
good luck.