Erm... I believe VW/Audi has variable programming for key fob behavior (for example, I've read of VAGCOM mods to make a VW behave audi-ish for remote window up/down...)
Is there an Audi-like behavior where you double- or triple-tap the fob release for all the doors versus the drivers?
What I'm getting at is whether there are discreet outputs on the body controller for each door actuator. If so, the programming may be a little fritzed and the drivers master lock/unlock input is working and the RKE is not.