Hmmm, you shouldnt have to initiate any security relearn, it should make you do security relearn before it lets you start the vehicle.

Thats really weird, when I ship a PCM the only things that need to be done are a security relearn before it will start then a CASE relearn to ensure misfire detection is correct. I know some people that wait 6 months to do a CASE so it should run just fine without it.