Just an update, the problem started when I left the car with my friend to do some work on it. He phoned me to ask how to un-immobilise it as he was having troubles, my guess is that he was pressing the remote lots of times, after this the problem occured. I contacted Cobra and did all the tests they suggested and the immbiliser seems to be working all right. As I said it all unlocks except the boot which used to, but won't lock at all, but will close the windows and sunroof.
Come on chaps help me out or I will have to send it to a VW garage and it'll cost me a fortune.