2001 VW Jetta Check Engine Light Problem...

I have a question for any other 99 and up VW Jetta owners. I recently had a Clifford Concept 600 Series alarm installed "professionally" because my car was burglarized with the cheap factory alarm. After 2 days of having the car back, my check engine light came on. I figured it would be some sort of engine problem and took it to a local dealership since its still under warranty. They informed me that they couldnt bring the fault computer in my car online to see what the problem was and like most dealerships blamed my aftermarket stereo and alarm for the problem. I was wondering if any other owners out there had the same problem, or if this is known to be a common issue. Reason I ask is the dealer tried to explain to me that my factory alarm is tied into the onboard computer and since its been disconnected to allow the Concept 600 to work, thats why the light came on. Needless to say I find this hard to believe, however I have seen stranger things on cars before in times past so I am not going to completely discount the dealers theory just yet. Any info would be appriciated...