Not sure if you've figured it out yet or not, but I just remembered had a scenario with security light on in the cluster, but the truck started and ran fine.
Earlier this year after a round of troubleshooting, I had Efilive flashed my ECM back to what I thought was my stock tune and ended up with a no-start condition and security light on. Suspecting my original tune file had been corrupt somehow, I figured it would be best to just start with a clean slate. So I sent off my ECM to SoCal Diesel to have it flashed back to a clean stock tune, with the vehicle security stuff turned off. When I got it back the truck started and ran fine but the security light stayed on in the cluster. Scanning with my CTS2 and with my Efilive Autocal showed no codes. Lorenzo@SoCal had me send the ECM back to him where he did some repair work on it beyond just a simple reflash. When I got it back, no more security light.
In my case it seemed that something in the ECM died or got corrupted after flashing, leading to the security light being on all the time. I doubt that's what's going on here, but I thought I would add that experience just in case others are reading this thread trying to diagnose similar things.