Water leak passenger and driver side, wet carpet

Check the bottom of your cargo area or front driver/passenger side, esp. after lots of rain if you have a 2011 Sienna van. We have an SE model. After a few consecutive downpours this past month - 3 days of pouring rain, I went to get the stroller out of the trunk. I noticed a few light large spots at the bottom of the rear cargo area. I put my hand down and noticed the area was wet. Strange because we don't store liquids in the back. I told my husband and he checked it out. Turns out the entire trunk/cargo area was soaking wet...right down through the padding underneath the carpet. It took 2-3 entire large paper towel rolls just to barely get the puddles under control and airing out the back. Luckily it was sunny for two days after we discovered the issue. The van started to stink from the mold forming ,and we were panicking since we have kids with allergy and asthma. Mold alert. The metal underneath the carpet padding had started to rust a bit. We just bought the car back in August of 2011. Took the car back to the dealer service center. First diagnosis, they called us next day and told us it would be $1290 because it was our fault one of the back windows latch was not sealed closed. Funny because we didn't even know we had back window latches and even when the service person in charge did a walkabout, no one noticed the window open. Ironic that nothing else was wet too from the top down. Not the back seats, not the strollers and kids knicknacks lying on top of the cargo area. So it's our word against theirs. I asked him if he was absolutely sure. If they had checked out all other posibilities and tested other possible entry points. He said that they were Toyota trained specialists and they were 100% sure. I'd read on some posts that after a few times of the same thing happening to another individual, they finally called in Toyota engineers to come look at it. I asked my service guy if they could do that and again, "ma'am, we ARE the factory trained technicians." After deliberating with my husband, we felt we had no choice but to have whatever needed done to fix the propblem properly to be covered under the warranty. Especially since we have one car and our kids are physically sensitive. After we gave them the go ahead, they were finally able to open up the mess (so before, it was just their best "guess" as to how the water had gotten in. They need our "okay" for the charge to actually open up the car). They tested the back and said it was water tight. Then they asked me if we parked on an incline. We do. About a 30 degree incline tops. Found out the water was actually coming in the through underneath the windshield "gutters" into a channel alongside the sides of the inner frame and flowing back to the cargo area. So guess what, we are covered under warranty. This is the kicker though, service person mentioned that yes, the water leaking in was probably happening for the lifetime of the car. He even told me that there was another same Sienna 2011 that had come in with the SAME issue. It is a design flaw/defect. So how do you fix that? NOW they are bringing the actual factory Toyota guys who will look over the repairs. Someone wrote on this board that they had just drilled holes underneath the car so the water could escape and not reach the back. I DON'T want holes drilled into my new car. And that person still had even worse water leak issues. Have been trying to find out if Toyota will in the least extend my warranty or do something about this car we just bought with a defect built into it. So, if you have a Toyota Sienna 2011 SE, have it tested. It's been two weeks since they've been "holding" our car. Said they are waiting for parts and are waiting for the Toyota factory guys to come oversee this repair. Wondering with the big recalls they have now if they are keeping this under wraps or if people are still unaware of the defect unless they parked like us on incline. I've read various posts where the 2011 Sienna leaked in the front driver and passenger areas which is worse because of the electronics and wiring. I am very concerned the problem will come back after reading some other posts on the web. Toyota has to do something for all of us who have just purchased new vehicles in good faith.