I had the same problem with my garage door openor.
My problem was that my opener has rolloing codes. Everytime you open the garage door the code changes. But only the remoteknows the new code. Its to keep thieves from stealing your code when you open your door and coming back later to steal your car. In order for me to hook it up to home link i had to disable this feature on my door opener but decided against it. Since some one has already tried to break in to my garage in the past.

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Dinan M3

2006 X5 4.4i Sport Current Vehicle
2006 CLS 55 AMG Current Vehicle
2010 FORD F-450 King Ranch Current Vehicle
2012 GL 550 Current Vehicle

1999 M3 Dinan S3 SOLD
2001 M3 Dinan S2 SOLD
2002 M5 SOLD
2004 X5 4.4i sport SOLD
2007 335 XI Lease ended
2009 E92 M3 SOLD