keyless entry reprogramming (car not starting)

I have followed the instructions in regards to reprogramming the keyless entry. After several tries, I was able to get the alarm keypad to lock & unlock the car. But when I used the key on the pad, the car would not start. The car would only start when I used the master key. Any ideas on fixing this problem? Any assistance would be very helpgul. thanx

The key needs to be programmed into the immobilizer system with a VW or VAG-COM scanner.

nick ... what instructions did you follow to program your key... i also have a new key and want to reprogram because old key is damaged... can i do this or do i need tool.. thx

I tried both of these instructions, so I don't really know which one worked. Here they are:
1. Insert the master key into the ignition lock & switch on the ignition (do not turn on engine). Lock the vehicle from the outside manually using the second key. Press button a or button c on the remote control one time and then wait at least 2 seconds. Press either button once again one more time. Switch off the ignition and remove the key from the ignition lock. The manual programming procedure is complete.

2. Turn the ignition to the on, not start, on position. Put the other key in the drivers door lock. Turn the key in the foor to the right (lock position) and hold it for 10 secs. Then immediately turn it to the left all the way, & hold it for 10 secs. you should here a tone, or beep, like when the alarm arms. When you hear this press the unlock button on your remote. There should be another beep to let you know it has programmed. If you hear the confirmaion tone, take the key out of the ignition and see if the remote works now.

Hope this helps, good luck.

Basically this means that i would still have to go to the dealer and have them program it, right. Thanks for the response

2. Turn the ignition to the on, not start, on position. Put the other key in the drivers door lock. Turn the key in the foor to the right (lock position) and hold it for 10 secs. Then immediately turn it to the left all the way, & hold it for 10 secs. you should here a tone, or beep, like when the alarm arms. When you hear this press the unlock button on your remote. There should be another beep to let you know it has programmed. If you hear the confirmaion tone, take the key out of the ignition and see if the remote works now.

Hope this helps, good luck.

FYI: I just bought a new remote and tried option 2 on my 98 GT and it did work. Thanks for the good information.