BMW dealerships used to have a key reader that could check the VIN & mileage of the key because the LCM sends this data to the key. But many dealers have tossed them under the desk or in a drawer somewhere So like others have mentioned...the key that starts the car is probably the original key and the door lock cylynder has been replaced.

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BMW Key Reader
The BMW Diagnostics Key-reader is a self-contained desk unit that reads the mileage from BMW keys. This is the true mileage from the heart of the ECU which updates the key every time it is used. The key-reader provides information on the mileage, the VIN and the key number to let users know if other keys have already been issued by BMW.
But this isn't the end of the world either because the door lock cylinder can be ordered based on the VIN (its coded)...and replaced...along with ordering anither key (doesn't have to be the more exensive remote either...there's non remote keys).
You can use
Welcome to realoem.com |bmw parts | bmw parts catalog| bmw epc! or
www.bmwfans.info to look up the approximate cost of ordering the coded door lock cylinder....for example, cllick this link and scroll down to #11...you would need the one that says
"catch with key code"...the lock cylinder will be keyed based on the cut of the original 4 keys that came with the vehicle from the factory based on it's VIN along with the same info kept to make a new remote or non remote key..again based on the vehicles VIN :
RealOEM.com * BMW E53 X5 3.0i FRONT DOOR CONTROL/DOOR LOCK