Its a common problem with the extended leather because the door card forms part of the seal. If you look where the rubber sits you'll see that some of the door card is actually outside the car. With vinyl thats not a big deal, but unfortunately the leather absorbs moisture and not only wicks it in to the car, but perishes in the process.
One of our members discovered that Audi actually revised these door cards later on and I think put vinyl on the outer portion with leather remaining inside. Alas its a bit late for that now.
The only solution I can think of is to treat the leather at the edges with a waterproofing agent so the moisture doesn't soak in. I'm going to be trying that on mine in the spring so will report back if its successful.
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