There is a explanation with pictures of how to resync the diesel with a Nanocom in the "How to" section. Faultmate extreme will be similar. Security learn only works on petrol engines. If you use a syncmate you need the correct one.
After searching the BBS forum, I've appear to have found the answer, I'II be returning to said vehicle tomorrow to hopefully resync the EDC/BECM.....if thats the problem...