When I bought the car there was no CD player. It had been removed. I fitted one out of my old car, Today I pulled it out again and pushed it back in and must have dislodged something as it was not turning off properly. After turning it off at the switch (not just ignition) the immobiliser is back working normally so I think I know where I have to look to sort the problem I will have to check the CD Player wiring.
Witchmaster's post in Immobiliser Led Stopped Working was marked as the answer