I had the leak on my 05 S too. Took it to the dealer and they packed that black mechanics putty/adhesive stuff into the windshield seal and everything seems to be ok at this point (two years later)

I have the same problem with my 2004 SE. My leak comes from clogged sunroof well drains. Open your roof and if you see pooling water at front, then you have the same problem.

The drains are inboard side of the plastic rails at the front under the wind reflector. You may need a flashlight to see them. They are just horizontal holes.

Air gun works well to blats the entire drain line drain but the tail of a cable tie will do in a pinch.

Hope this helps.
My dealer was no help.

We've been to the dealer numerous times with leaking issues. It started with water coming through the sunglass holder. First they told us that debris was getting in causing it to get clogged. They tried to tell us that we shouldn't park under trees (in other words, move). I laughed this off since the dealership is right next to a wooded area. We called the dealership and not service an got that fixed.

Next we found the entire rear well soaked after a period of heavy rain. The replaced some plugs in the back, which reduced the leaking, but we still saw water come in through the rear vent window. They attempted to repair it and ended up pushing the window out so it would get hit by the rear sliding door. Just got the window replaced.

I'm interested to see what happens this fall as more "debris" comes down.

I think one of my problems is that my dealer's service department is miles away from the sales office.

2005 Quest SE w/ sky view. Same problem sunglass case filling w/water faulty windshield bead from factory.Dealer had vehicle over a month could not find a windshield to fit correctly after 4-5 attempts. In the process now trying to get into new vehicle moisture ,corrosion and health risk of mold two young children one now uses a inhaler since I purchased brand new Quest 12/22/05 currently 5300 miles on vehicle. Is it just funny timing or is the water problem (mold) the issue here???

Yes, I have the same problem in my 2004 SE. I just bought the vehicle used and discovered the problem with the first heavy rain. It seems like the water is pooling in the sunglass holder. When you hit the gas or go around corners it streams out from the holder. Very annoying. Please advise if you discover solution.