Hi Pit Dweller,
Just picked up on your reply to this fault.
I renewed both my drivers side doors recently and this fault on my B6 (2007 Estate) has only cropped up since. I never touched the tailgate locks or went anywhere near it mechanically. All the doors electrics/modules/motors etc were transferred from the old doors. All seemed to be working perfectly after the damage (deep score/tear along the side very low down below the 'inner guts'). Windows, mirror and door locks all worked perfectly after the damage and before the doors were replaced.
Can you give a bit more detail on replacing his module? I note you've 'replaced many', so are you a VW Tech?
I have VagCom and have used it many times so is it possible to replace the unit myself and recode?
Cheers,
Steve