Right found a Fix after speaking to some specialists over the phone, they were good enough to provide the details. Thought I'd leave the instructions for anyone else who may have the problem in the future.
This was for a Rover 214 Cabriolet L Reg. This will work for the older models that don't have Key fobs.
1. Remove Negative from battery
2. Remove Positive from battery
3. Touch the wires of Negative and positive together. This completely removes the charge from the car. This is the wires to the battery your connecting together not the battery itself
4. Insert your key in the ignition to position 2.
5. Reconnect your battery
6. Move key to position 3, car should start.
When the battery dies the car thinks someone is trying to steal the thing and the immobiliser kicks in. Following the above in effect resets the system. This fixed the problem for me. I guess we will have to do it again if the battery goes dead.
The specialists told me a few other things if this doesn't work.
micro-switches in the door as the previous poster mentioned. Under wear and tear they have a bad habit of bending. Apparently the door has more then one and its just a case of locating the problem Finding a spare or in some cases bending them back.
Method C - I not sure if he meant doing this after following method 1
Make sure all the door, windows, bonnet etc are shut secure then a bit harder the usual unlock the door. He mentioned something about the mechanisms after wear and tear being beyond the turning points.
Check the fuses by the battery. Some of these are associated with the alarm and immobiliser.
Hope this helps.