Thank you very much for this which I can pass on to my garage. Could you please clarify - In 1, when you say this can cause this type of issue, did you mean having the audio unit programmed or NOT having it programmed?
It seems that as my Sony is not a Ford unit it can't be VIN coded to the Gem. However, the local Ford garage still says that this shouldn't cause the alarm to go off. My garage is currently looking at doing something with the wire that used to connect the original audio unit with the Gem.