Ok so currently got 2 keys and one remains unaffected so not stranded as we were.in town with both sets but my key today unlocked the car released the steering lock and started the car but after 2 seconds killed the engine with the warning immobiliser active. Allowed the engine to restart but again only for 2 seconds. The other key works as normal thank god. The non working key is new about 2 months ago from the aa and has worked fine since then on at least 10 occasions........ideas

You'll need to get Skoda to program it, it can be a pita tbh, took VW mechanics an hour to program mine on the Passat so the AA guy probably didn't have the full monty equipment to program it fully,

 

That or the battery has moved about and not making a contact properly, check the handbook for a programming sequence also, sometimes you can put the key in so far and hold XYZ buttons and it restores itself, can't promise cos I don't have the book for it but it might help.

You didn't have both keys close to the ignition barrel did you?  If you did then that could be the problem - the way the immobiliser works is that the transponder chips pick up an electric current from a coil around the barrel and transmit their ID to the car.  If both transponders get activated at the same time then you can get both transmitting at the same time, which means the car doesn't receive either clean signal.

 

If nothing else has happened it sounds like you have a faulty transponder in the key which doesn't work... I can't see how just one key would get forgotten.

There is no power supply to the transponder, so the battery won't affect it.