I have had 'phantom sunroof' myself. I'd had the battery off, and the same issue. I sat there, and patiently held the button in for a few seconds, for nothing. Also tried moving the switch in various positions, which, again, resulted in nothing, maybe the odd 'tick' and clunk, without anything much in the way of movement. Driving down the road, I sat there and decided to give it another go, after holding it in for what seemed longer than necessary, it started to shut. Personally as you've eradicated all the other usual possibilities, it does sound like you just need to have a go a few times. Maybe trying it with engine running, if no joy, switch off, lock car, unlock, then try again, that sort of thing. Also worth trying the 'auto-close' function. Get out of car, press and hold the lock button on the remote, see if that closes it. (Having a window ajar will show you if this is working, as this will shut also)
I was at the point where I'm thinking 'ahh this is buggered, I've had it; when it just decided to work, so hold your nerve, and don't worry
(oh, mine's a 2.5 TD W reg, too)