Just maybe this will do the trick...
Try reprograming you remote key with the guide below, If unsucessful Replace Fob battery and try Again!.
VW/AUDI/SEAT/SKODA
Remote Control Programming (1997 ON)
Procedure
1. Switch Ignition ON and leave the key in the ignition.
2. Mechanically lock the vehicle using the Drivers door using a second
key.
3. Using the remote control press the Unlock button once, and the horn
will sound once.
4. Wait 6 seconds and press the unlock button once to activate the coding
procedure. The remote control will now be programmed.
NOTE : When performing programming on additional remotes the procedure
is the same, except you press the unlock button 2, 3 or 4 times for the
different remote.
For example : If programming 2 remotes press the unlock button twice with
a 1 second interval between each press, repeat for 3 and 4 remotes.
5. Switch Ignition OFF.
6. Remove key from ignition and check for operation.
7. The coding procedure can be repeated up to 4 times for additional remotes.
8. The ignition must be switched OFF between programming each remote
control.
Gez, November 2010