Security light flashing

I have an 00 GTP and just got done swapping the engine in it. Started engine up and now I have a security light that stays flashing for 10 min or so before it goes out. Car starts up, runs fine, and no codes. Did the security 30min relearn procedure and that didn't fix the problem. Where to now? Didn't have this problem until after engine swap.

I'm starting to think this doesn't have anything to do with the engine swap, but more with the battery being disconnected for a long time. When I disconnected the battery changing the Cam position Sensor before, it did something very similar, but would die after 3 secs.

I'm also thinking I may have done the relearn wrong. I started this process right after shutting the car off, without waiting at least 30 seconds. Below is the relearn procedure I followed. Do you think not waiting after shutting the car off and starting the procedure could have effected the process?

With a master vehicle key, turn ON the ignition, with the engine OFF.
Observe the security indicator. After approximately 10 minutes, the telltale(security light) will turn OFF.
Turn OFF the ignition, and wait 5 seconds.
Repeat steps 1-3 two more times for a total of 3 cycles or 30 minutes.

Important
The vehicle learns the key transponder information and/or passwords on the ignition switch transition from OFF to RUN. You must turn the ignition OFF before attempting to start the vehicle.

With a master vehicle key, start the vehicle. The vehicle has now learned the key transponder information and/or the ECM has now learned the fuel continue password.
If additional keys are required to be learned:
Adding Keys
Important:
• To initiate, this procedure requires that a learned master key be available.
• A total of 10 master keys or valet keys may be programmed to a single vehicle.
• This procedure adds keys only. The procedure does not erase previously learned keys.
• The keys to be learned must duplicate the mechanical cut of the current key.
• If more than one valet key is to be learned, immediately precede each valet key with a learned master key.




With a previously learned master key, turn ON the ignition, with the engine OFF.
Turn OFF the ignition and remove the key.
Within 10 seconds insert the key to be learned. Turn ON the ignition with the engine OFF. The vehicle has now learned the new key

Well it's definitely not a relearn issue, tried 3 times the other night.

I find it curious that this happened after a motor swap, but then previously when I had the battery (http://www.walmart.com/cp/Auto-Batteries/1104292) disconnected to change a cam position sensor the security light was flashing, car would start and die with in 3 seconds with the master key, but would start and run on Valet key. I got a new key and did the relearn to fix that problem, but all the old keys also were able to be relearned again, so I don't believe the key was the problem. So now after reconnecting the battery this time, the security light blinks but the car starts and runs fine with the light going out after 10min.

I'm surprised there hasn't been a class action suit against GM over this issue. There are thousands of posts on the internet, but no one ever posts what the exact fix is and the cost of the repairs range between $100 to $1000 with some never being fixed. Ridiculous.

Anyone have any thoughts?

From your owner's manual, do you know which Security system you have?

PassLock or PassKey II or III?

I have the Passkey 3, PK3 on key.

If that light is flashing, then a code is set....problem is, you probably checked with a code reader/scanner, that only reads "P" codes, Powertrain codes....what you need is a scan tool capable of reading "B"(body) and "U"(communication) codes....

When the engine was changed, it's quite possible, a wire harness was not connected, or a wire was pinched in a harness....

Thanks for the reply. I'm in the process of trying to find someone with a Tech 2 or scan tool capable of reading the other codes to see if it will point me in the right direction. I'm siding with it's either the lock cylinder, ignition switch, or the theft deterrent model. Just a matter of which is the culprit. I think the root of the cause was more due to disconnecting the Battery and not motor swap. I was very careful with the wiring, and have been over all of it twice now thinking exactly as you are. I had a similar problem the last time the battery had been disconnected for an extended period of time, with it not recognizing the key to enable it to keep running.

Here's a little interesting update. I swapped out the theft deterrent module and that didn't solve the flashing security light, so out of curiosity I disconnected the theft deterrent module plug and the security light is not flashing anymore and the car still starts and runs. LOL I realize it's not supposed to start and run, but it does and I don't have to look at the light flashing for 10min.

Anybody got any idea of what is going on with it?