An update from my earlier post; I also see several others reporting the same issue - it's rubbish isn't it? My Kombi has been back to the dealer (Basingstoke) 3 times now. The last was for 4 weeks while they investigated the problem! They also had 2 new vehicles with the issue. The conclusion - prolonged rain (hours) allows a build-up of water past the top seal, it then overflows past the inner seal. Cause - the sliding door alignment is incorrect, particularly the O/S. They have fully adjusted both doors inwards and replaced the top outer seals, a new batch seems to be a slightly firmer rubber extrusion. It should be obvious the top outer seal is compressed when doors are closed.
It seems there is at least a batch(es) of Kombi's coming out of Germany with poorly fitting doors. So far I've not seen further ingress, but it's not yet rained significantly. Under consumer rights, I've reserved the right in writing to reject the van if it returns.
Should say my local dealer has been very good and diligent, even though the time scale has been frustrating. If you're still having problems push your dealer to move the doors inwards & replace top outer seals under warranty. If your seats are water stained they should be replaced under warranty. It's a VW problem, they need to deal with it and compensate where applicable.
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