Aidy...
Tell them to check the CCM Module. (Central convenience module).
Then swiftly suggest that they update the firmware and software on the module. Our MK5 GTI did this exact thing. Its a quick fix. A matter of two hour download of the software from germany.
The reason it does this is because the CCM computer is American and the actual electrical systems are German... The two sometimes conflict and you end up with this as a result.
Being a MK5.5 (har har) I imagine they would have simply carried over the same CCM module to the MK6. The module itself control lights, central locking, heated seats... the works. Its like the ECU for comfort.
That should do the trick. If it doesnt... Simply reset the onboard computer or disable auto windows up or down.
Mike