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I have a 2001 Passat and have also had the same problem for the past 5 weeks - excessive amounts of water on the rear back floors.
After bringing it in four times, they have diagnosed it with two problems:
-sun roof leak (the drainage tube was somehow misplaced) and
-faulty pollen filter (the sealant had worn away).
I would definitely take it to the dealer as soon as possible, the water leak has started to affect the wiring of my car and I'm told I have to have the comfort control module replaced (which is going to cost $600), there is also a transmission control module in the same area which could be affected by the leak.
What is the A/C problem - I haven't heard of that --I've run my A/C to clear the windows so I'm wondering if there could be any linkage.
please keep me posted on resolution of your issue.
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