Hi Caracola,
I have an '04 LS430 and had trouble with the HomeLink in my car. When I first got the car home, I proceeded to program the HomeLink for my Overhead Door openers with Code Dodger. Button #1 setup fine with door #1. Button #3 would not setup at all with door #2, so I tried Button #2 with door #2. Button #2 setup, but operated both door #2 and also door #1 at the same time. So, I asked the dealer to replace the unit, thinking it was faulty.
The dealer had to order a replacement. They installed it yesterday and I couldn't setup any doors with any buttons, so I called the dealer. I had programmed my '99 LS400 and other remotes with no problem, so I thought I was experienced enough that it wasn't an operator problem and thought the new unit was defective. They sent a technician out to my house. He was able to get it to program how I wanted it for both doors, and he used the extra remote I had in the process. I could not get him to explain what he had to do, which really frustrated me. (That's why I did a search on HomeLink AND Lexus and found your post.) He said the manual is not clear and he has suggested changes, but Lexus has not used them.
In any case, maybe the dealer will have to send someone out to see the problem if it occurs again, which I suspect it will. Keep a log of what you have experienced to document the situation.
Moderator : I think we will hear more about this subject and it should be moved to the Technical section with it's own topic.
