Make sure your homelink is on the same frequency as the transmitter, if it`s not, then it`ll never work. I had this problem with mine, US homelink but I`m in the UK and we use different frequencies. In the end I gutted the homelink box and hard wired my own transmitter in to the homelink box..

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X5 3.0D 2003
Mods:
Webasto telestart remote kit
Aluminium running boards
Tv in motion & Aux input lead, Ice>ink to Ipod 3g.
DVD rear headrest screens and dvd sytem integrated in to main tv system via aux lead (watch tv or dvd in front and back)
Homelink Gate Opener, Chrome Grille Kit, chrome tailgate handle, Chrome Guage Rings, Tunit V-CR 086
Standard:
Bluetooth, comms pack, sat nav, sports pack, sports seats, dimming mirror, electric folding mirrors, memory seats, heated seats.