I changed the ignition lock cylinder, had 2 new PK3 keys made.
I programmed the Pk3 keys and they both worked for a few days maybe a week or so.

Now the security light comes on when trying to start the car.

What else could cause this and how should I go about correcting it?

Have you tried a complete reset of the system ?

http://www.justanswer.com/pontiac/3u4em-2003-pontiac-aztek-replaced-battery-starter.html

I've done the complete reset thing. I took it to the local community college to let their automotive department look at it. The only thing they can find wrong with it is that it doesn't recognize the key. I've tried the old lock cylinder and key and new lock cylinder and key with the 30 minute relearn procedure and it won't recognize any key. I'm getting ready to replace the module that goes around the lock cylinder. I'm thinking at this point it may be at fault and can't see any key that is put in there. My question is that if I replace the reader/exciter module that goes around the lock cylinder, will it need reprogrammed (the new module) or will I just have to try the 30 minute relearn on the keys to get it working again.

Actually, it sounds like bad parts and/or poor fit either of components or connectors.
If you're using original equipment replacements from the dealer, you should have a warranty, but if you're using after-market replacement parts, you will still need to contact the vendor for any attempt at warranty replacement.