To oversimplify: every key has a little circuit in it, and that circuit is unique for each key. The truck's computer is programmed at the factory to recognize the keys you're given.
If the truck's computer doesn't recognize the ID that's encoded into the key's circuit, it pops that code. There may be other reasons why the code would show up, but I dunno if any apply to our trucks or not.
So theoretically (especially if that key won't start your truck), the computer doesn't recognize it. Either something happened to the computer or the key, or that's an aftermarket key that hasn't been programmed into the computer by a dealer yet.
EDIT: If you're not having a problem starting the truck, then maybe they've extended the immobilizer system for other stuff. Some companies do (*coughVWcough*).