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My 2009 just started doing the same thing last week. I also checked the drain tubes and poured at least 2 liters of water into the tray, could'nt recreate the leak. there were some tree buds in the tray, maybe caught between he seal creating a small leak?
 

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Either way you open the roof does'nt seem to matter, although the rubber and felt seal is'nt as strong or resiliant as the one on my wife's Audi. Also you'd think that filling the tray with water would recreate the problem but no. Can the roof be manually adjusted forward to put a little more pressure on the seal?
 

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Ok, Good news, and bad! Good news is I tore everything apart and poured water in the tray and found out were my leak comes from. Do you park on a partial downward slope? Now the bad. Because of the poor felt around the moon roof it lets water in very easily, just put a hose on the roof for a few minutes then check how wet the tray and wind screen are. If their like mine, they are very wet. So when parked in a strong rain the water fills the tray faster then the tray can empty causing water to go over the front of the tray and onto the headliner and into a divot by the map light were there is a slight cut in the foam backing letting the water soak into the cloth material. One reason it may also drain slow is it may only be partially clogged. Mine seems clogged and the passenger side is most likely detached causing a leak on the floor. My Touareg came from Arizona and the dealer said the tubes are probably dried hard! Good Luck with yours, mines on the way to the dealer (1 month left on warranty)
 

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The area seems to be the full front of the sunroof tray! The sunroof rain tray is only screwed up from the bottom of the sunroof and does'nt make contact or seal against the bottom of the roof sheet metal. One service advisor said to possibly try some RV seam caulking or window sealing bute. To push a string of this semi-soft material up under the leading edge of the roof and around the sides in a continuos bead far enough back as to not interfere with the glass but to seal the gap between tray & roof. I'm not sure if a regular rtv silicone would work as well. P.S. all my drain tubes check out fine so the overflow from the front tray is my only answer, guess i'll try the strip of bute caulking.
 

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Photos of leaking area

This is the spot my Touareg leaks at.
Car Vehicle Automotive exterior Automotive design Vehicle door

Use a complete length of windsheild sealing bute, or RV
seam caulking to close the gap where the rain tray comes in
contact with the underside of the roof. Remove the pop-up
screen to access the front of the sunroof and place a bead of
rope sealant under the sheet metal and back far enough to seal
the tray gap. one long strip that extends far enough down the sides. make sure not to cover the front drain holes!
Vehicle Car Automotive exterior Auto part Family car
 

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For all of you who have had this sunroof leak onto the headliner area by the map lights, here is the news from VWoA! It is a known problem, covering all Touaregs up to 2010. Service Bulletin Number 60-07-03. weather your vehicle is out of warranty or not dealers should remove the headliner and replace the sunroof seal to body. But remember we are talking about the dealers, not VWoa itself!
Good luck! I'll report back when it starts raining again.
 

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rso2011, I see your in Seattle, try campbell/nelson in north seattle. They fixed mine and so far it seems to be working. Remember, this is a service bulletin not a full recall so it allows VWoA to say nothing is wrong were just straitening things up a little. You know recall is a 4 letter word in the auto industry. anyway try them, they have the full 411 on the subject and seem to be very pleasent to work with, which in VW circles is amazing.
As for the rope caulking I was told, but did'nt need to use it. But to put a string of rope caulk up half way up one side across the front and half way down the other up under the leading edge of the rain tray where the tray meets the bottom of the roof sheet metal. This was info gathered from other VWoA areas (NOT!) Campbell/Nelson VW.
Good Luck, try the dealer first, then if all else fails, try yourself.
 

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RSO, sorry for the late response, I've been out of town. The person who fixed my Touareg at Campbell/Nelson VW was service manager Peter Szegiet. I didnt personnally take with him since my wife dropped off the vehicle, but I asked for his card. Hope this helps, if you havent already gotten the problem solved.
 
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