Does anybody know if the control modules for a 2002 TL can be programmed for custom capabilities?

When my sweetie bought her TL, she discovered that if the headlights are on, removing the key does not shut off the engine. Also the parking lights are on whenever the key is in the run (on) position. The dealer told her these 2 features were optional features added to the car. Also, the security system does not activate, although the keyless entry works, and will honk once when holding the panic button. Another oddity is when unlocking the doors, the parking lamps flash twice and while they are flashing, pressing the unlock button the 2nd time doesn't unlock the other doors.

Everything seems to work, the just don't work as expected. I have the service and electrical manuals, but with the batch of gremlins, I'm not even sure where to start first, and know the projoect would be sizable for what are not major problems. It is almost as if the functionality has been altered (such as the parking lights or headlight timer). I am very well versed in troubleshooting of electrical problems, but am hoping someone has some starting ideas. If I had a set of the control modules (driver door, driver fuse panel and passenger fuse panel) those would be the first things to try. The problems are too consistent for a floating ground, but i haven't ruled that out either.

Miner