This sounds like a problem with the EIS, I am unsure why this key would cause a problem with the EIS (electronic ignition switch) like this.
The key has a transponder inside, actually 2 of them, one for a fixed code, which identifies a particular key to the car, and another which contains a rolling code, which changes every time the key is inserted into the EIS. There are no memories in the key in the common sense. On the newer cars, starting with the 203 chassis, the EIS sends info to the door control and seat modules which will adjust the seats and mirrors to a particular key number, also I believe the climate controls and radio settings will also be affected.
The EIS acts as a gateway between the engine CAN bus and the interior CAN bus. I believe the signals from the brake pad wear sensors is recieved by the traction control computer and the warning itself is relayed to the instrument cluster via the EIS (gateway). Again, no reason I know of why a signal like this would be transferred to the instrument cluster incorrectly and with only one key, not the other. I don't think there is an easy solution to this, going to have the dealership look at it.
Gilly ps I would also be concerned about the missing keys. The missing keys can be blocked by the dealer by using the SDS, I would look into finding out the missing key numbers and having them blocked.