I have a 2010 JKU and have the same problem since day one. Be honest I haven't really worried about it. I take the carpet out on occasion and throw it in the dryer. The carpet comes out in 2 minutes. I figure it this way, I go through rivers, streams and have been caught in the rain with no doors or top on. It is a Jeep and the design of the removable top, (which makes it iconic) is not like a typical convertible car. On a Jeep you are removing the complete top, doors and the plastic frame door surrounds. So, I really don't no or have attempted to isolate the problem.