I had similiar problems with my 03 X5. I have Craftsman Door openers, here is how I did it. Cleared the programming by holding button 1 & 3. Then pressed and held button 1 and at the same time press the appropriate button on the original remote. when the light on the homelink flashed fast, I released and then went to the garage door unit and pressed the program button, returned to the car and pressed button #1 of the homelink and.....the door opened. Did the same with the other door. Seems as if you need to program the HomeLink with the original remote first and then you send the signal from the Homelink to the actual opener. Hope this helps.