[PsYcHe]

The only one I can think of is that the immobiliser has forgotten about the key (or never knew about it in the first place). I think there's a VCDS procedure to re-code it, or you may need to speak to Shark Performance (or see if ben at AVP can help).

Found the link: http://www.ross-tech.com/vag-com/cars/immobilizer.html