My garage door has a scramble code. After programming the homelink, I have to go back to the garage door opener and press a button on the back of the unit, then run back to the truck and program it with three or four short presses of the homelink program button. I believe this is covered in the homelink program instructions. Homelink site provides help, and they are also helpful on the phone.
http://www.homelink.com/training/train.taf