How do you tell if you have an alarm system? I did not think mine had one, but my wife used the "spare" key to drive it yesterday, as soon as she unlocked the truck with it, the horn started going off and the lights flashing, those stopped as soon as she started the truck and she was able to drive with it and it did not shut off in 4 seconds like bain64's.

 

You have the alarm then it sounds like. My truck can be locked with my remote, key or door button, and unlocked in any fashion and I never get any horns or flashing lights (except for the flashing parking lights when the doors are unlocked with the remote). You should be able to disable the alarm, but theres no reason to with a dealer working on the truck. They should be able to get you a key fob that works properly with your alarm equipped truck.
The 4 seconds bain64 was talking about is a delay before the alarm system is set off; if the door is opened without the remote, the alarm will be set off 4 seconds AFTER the door was opened if the engine hasnt been started.

 

So the problem is probably the idiot's at the dealer don't know what they are doing. I'm considering getting a carfax for the truck but I don't want to spend the money. It would be nice to know the history of the truck.

 

In all seriousness, get your money back since they didn't do anything, and if they try and say you still have to pay for labor don't let that BS fly. I got my 2-way viper alarm for around 300 and it has more than enough features... I LOVE IT. At least look up some info on it, it's just so much better than the dealer doing it.