when you say key programing do you mean the "infra-red" central locking key?
if so... im sure the infra red module in the sunroof panel has its own memory and is not linked to the ecu in any way...
if you read the fiat punto handbook! it says you can only programme new keys when the car is FIRST bought and brand new, in any other case you will have to go to Fiat dealer to programme any extra or current keys, its a way to stop any "theif" re-programming any new keys to your car.
ive just bought my punto, the central locking works "manually" but not via the infra red key remote!!!