Yea you may be unable to program it due to the issue w/ the passlock system....I've read a little about bypassing it but I can't really offer any advice on it at this time. You'd be best off doing some searching about the subject. I'm going to go back and do a little more reading on the system....the bad part is that you can't hardly do dick as far as troubleshooting unless you have a tech2. Just for kicks check fuse "TBC" (10a) in the underhood fuse panel and fuse "IGN 1" (10a) in the panel left of the dash. They both send 12V to the BCM. I'm sure you've checked but make sure those battery cables are in good condition as well.
I don't doubt the Autotel is a decent scan tool but I don't think there is a hand held unit out there that will read the body control module codes but I could be wrong.
BTW.....if I open the door to my truck the security light is flashing....when i put the key in the run position all i have is a battery light. For whatever good that may be LOL.
bossier62guy's post in another passlock mystery was marked as the answer