Do I understand that you keep finding the battery flat, hence the clicking. It could be related to the RNS510, if it doesn't shut off, it will keep drawing power and drain the battery, particularly if the battery is on its way out. The RNS should shut off after 20 seconds or so. Had this problem when I retrofitted a MFD2 into my Mk5, it needed a later model control unit.
I would have thought that this would not be a problem with the Mk6, but it may help to narrow things down, it is possible to check using VCDS that the unit shuts down correctly, I will try and find the procedure and post it.