Jetta Cli '96?

The alarm does not want to arm with the remote. the remote does function, as the red light comes on when pushing the button. the main box has two plugs at the back, and I've just unplugged it to disable it completely. when I re-connect it, the central locking kicks in and the immobilizer also kicks in. if i open the door or try to start, the alarm goes. how can i get the remote to switch it on and off again like it use to?