What were the fault codes on the scans?
The immobiliser check is in the dash, using the K-line it talks with the ECU which then allows engine start - or not.

How did you get it scanned? All units or just ECU?
Have you had the keys rematched at all? Might be a fault in the instrument cluster. ECU itself is more rare and you normally have fault codes relating to 'internal electrical fault'.