Have you made sure your drain plugs are properly installed? Mine weren't when I bought the jeep, and my girlfriend ended up with a very large puddle courtesy of the even larger puddles we were driving through. She took it in great stride and enjoys the jeep - signs of a keeper to me
I have since removed the drain plugs completely, and have them in the glove box should I decide I need them. The rain was being forced up the drain hole because the puddles were rather large. I guess that the next time it monsoons here in Florida, I'll put them back in.