This is a long shot, but it was my problem for a while. I have an "Overhead" brand garage door and was trying to program my car buttons. Tried forever and failed until I saw a small footnote in the garage door instructions. I was using a 3 button remote to try to program and I was trying to program the door that opens with button 2. The footnote said that "you can not program a car using button 2 of the remote". No reason was given. To get around this, I temporarily reprogrammed the remote to use button 1 to open the door I was trying to program and then programmed the car using button 1 on the remote to open door 2 and everything worked ok. I have no idea what is behind this restriction, only that it is a real restriction.
Like I said, it's a long shot that this is your problem, but sharing just in case.
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