Windshield Leak?

[parshal]

We bought a '97 4runner at the beginning of last summer and noticed the windshield had a whistle sound at speed. This summer, we started getting water on the driver side floorboard when it would rain hard. This was not a small leak of water but left the entire driver's side floorboard soaking in water. We took it to a windshield repair place (the windshield was new when we bought it but that's common out here) and they said they found a place where the old sealant hadn't been removed. They fixed it, resealed it and the whistle is now gone but it still leaks. We're going to bring it back to the windshield place to have them look again but I was wondering if there is anything that people can think of that would cause this. I had an old mustang that used to leak when leaves got in the air vents but we don't have leaves (to speak of) out here.