Now why would they do that unless the shelf stock was done with the new process? Why jerk people around?
On a different note, I bought a used certified GM 06 Chevy Avalanche and have had it to 2 different dealers for warranty issues and BOTH dealers treated me like family and fixed the problem right the 1st time. 
No hassles, just friendly "how can I help you" service. Guess what company I'm buying my next vehicle from?
My guess is that it was the only way to legitimately get rid of the problem from an accounting point of view, it has gone on way too long for them to not know they were sending out bad tins. Often I think manufacturers are driven by an accounting mentality.
On the question of where you're buying your next vehicle, I would hope it is from the "dealer" that is closest to your home providing you the best service product. IMHO, this keeps your tax dollars in the area in which you live and supports the business doing the best job for you.