Hi, welcome to Just Answer.
Is the alarm horn ringing? Or is it the enigne that will not start?
I see...you should be able to disarm the alarm by turning the ignition key in the driver's door twice in the unlock position. But if that no longer works than the switch in the driver's door may now be faulty. You can also disarm it through the trunk lid key lock. If this is an aftermarket alarm system, it has to be removed from the car, it may have entered passive mode recently, which would explain why it arms now. Also, if it is an aftermalrket alarm, there may be a valet switch under the driver's or passenger dash that can be switched ON, with the key in the ignition to ON and the alarm should remain disarmed until you switch the valet switch again. For the factory alarm, if the unlocking of the doors no longer shuts it off, unfortunatly it will need to be either diagnsed at a VW facility, or a new master key with the transmitter purchased and programmed.
Aftermarket alarms are installed at the dealer or at stereo/alarm shops...usually if it is the factory alarm going off, than the engine does not start as well (but that's not always true). Aftermarket alarms will not disarm with the remote/key that came with the car, they have a seperate remote and a switch under the dash (valet switch) for disarming. If it is the factory alarm, you should be able to disarm it through the trunk, if you use the driver's side door to disarm it, than the switch in the door goes bad over time and no longer works. Let me know if your still having trouble with it...