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I still think something was fried or otherwise tweaked or shorted with that remote starter. It's the only outside non-factory variable. The chances both remotes would be bad are pretty much zero. I'd pay the $200 or so diag fee from the dealer
I have 2 remotes and both are the same only sometime work, I guess no any other choice, new remotes.
I agree with E46CT for what its worth. Both remotes with the same issue...no way. Issue is with the car and like said, ive never read about a problem like this where the member did not have aftermarket systems installed. Somewhere somehow thats the issue.
Its returned to stock now so dealer is a good choice to diagnose. Worth paying them as well....starting the car and getting in it is pretty darn important.