I have recently found out that the standard fit M3W immobiliser key fob can loose its code if not used periodically, there is no battery in the fob. A spare key fob that had not been near the car for a year or so was tried and wouldn't deactivate the immobiliser. The fob normally used to start the car worked fine.
The supplier was contacted and was more than happy to replace the fob for about £50. Not so much an issue if you have lost or damaged one but there was nothing physically wrong with it. Eventually they conceded that the fob could loose its code if not used occasionally and that it could be re-coded from the transponder under the steering cowl. There is a rather involved procedure for this that I can pass on if you PM me, it will be on the MTWC website soon. You do need to have at least one working fob for this to work. I suggest it would be a good idea to use all your fobs to start the car every 3 or 4 months.
If all this fails you can always remove the immobiliser from the system by making and fitting an immobiliser jumper plug, as detailed on page 66 of the M3W parts list Ver 5.2 item C-47 on the RH side. You will also need an AMP Multilock 070 12 way male plug and pin set. Morgan could supply these at one time but don't seem to be able to now. I got my plug from
www.simtekuk.co.uk and they were very helpful. With the jumper fitted the immobiliser is out of the system, handy for diagnosis as well as a small, light item to carry in your spares bag that may just come in useful one day?