Problems with Theft-Lock

I have recentley reinstalled my stock sunfire stereo deck into my car. I had a problem with the wire harness, and once i replaced i re-wired and when i went to take it in to the dealer to re-insert the vehicle code to allow access to my radio, and disarm the theftlock, the computer at the dealership could not read my deck... anyone kno what could be the reason for this problem....