If replacing with the same type of battery then it needs to be registered otherwise it needs to be programmed.
http://www.e90post.com/forums/showthread.php?t=542737
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If no codes are being thrown use Chevron Techron fuel injector cleaner (concentrate). It solves rpm fluctuating upon cold start-up. Also, for most BMW problems start off by scanning your car with the Peake Research Tool. It contains the actual BMW codes. If you want to register a newly installed battery for free (just buy a $10 cable) and google/download BMWLogger