Do you have the doors open while you're doing this? Don't think it makes any mention of it in the manual, but I think I had mine closed when I did mine. Also, when you say the doors were unlocked, are you saying they had been unlocked, or that you pressed the unlock button?
My guess is that you're timing out. Get in, close the door and lock the truck. Wait a few seconds. Press the unlock button, inset the key go from OFF (1) to ON (3), counting every time you hit the 3 position. Stop when you hit the count of 8, which should end you at the 3 position. This has to be done in under 10 seconds. Do it in a fast, but controlled rhythm. I think I was hitting the 3 position every second.
I made sure to "act" out all the steps before attempting, since stopping to read can cause a time out, and have you restart all over.
I'd post a video of it, but I don't know where my other key fob is. Also, I don't think you need to have 2 key fobs to do this procedure. This should only be the case if programming keys, since it's a safety feature of PATS II.