Holding the handheld transmitter against the mirror housing is the tip that did it for me!
Just installed a Chamberlain garage door opener (Model LW3000EV purchased from Lowes). My 2013 E92 M3 would not accept the code from the handheld for the new garage door opener.
Read about Chamberlain MyQ Security+ 2.0 and lack of backward compatibility
with my BMW and so purchased the HomeLink Compatibility Repeater (from Amazon).
Despite not having had any problems previously programming the vehicle to operate several other garage door openers (e.g., Liftmaster and Chamberlain), could not get vehicle to accept code from the HomeLink repeater handheld unit (regardless of where I positioned the handheld transmitter).
After reading this thread, held the transmitter against the mirror housing and it worked the first time. Was able to complete programming in 10 minutes after that.
Thanks for the tip - I was getting ready to send the repeater back and abandon use of the integrated HomeLink capability in the car. It's much nicer to have one less item kicking around in the car
.