Water Leak

We have an '06 Safari, 28 ft. purchased used summer 2013. We are paranoid about water damage after spending $6000 replacing the pressboard floor in our 06 Bambi last summer as well. Returning from a trip this week we find moisture under layers of floor covering in the "trunk". After removing all the contents I find there is a plywood (luckily not pressboard) subfloor, then padding, then carpet that extends from the bedroom into the trunk, then about 10 ml. poly sheeting covering the carpet then rubber mats. The poly was attached thru the carpet and pad into the plywood apparently by the factory. I know the previous owner did not do this, he barely used the trailer and kept it covered and very clean. We ripped all of this out and the plywood was damp from the door about 12 inches into the trunk space. To me this pattern indicates water is entering from the seal at the trunk "door". Our seal appears to be intact and pliable, but the door is slightly less tight on one side. (now fixed) Why any factory in their right minds would install this carpet layering into the trunk and then cover it with plastic is beyond me. If we had not been inspecting, we would never have noticed the water intrusion and it would not have dried out satisfactorily. If you have not checked for leaks, I strongly urge you to do so. Does anyone have experience with a leak in the door and ideas on how to really fix it? This apparently was the problem with our Bambi.