When I opened my door I noticed the middle hinge, what looks like a rubber boot seperated on both my front doors, check yours and see if yours has done the same. Will this be an issue? Like water leaking into it.

FYI: on my newly bought 04 XLT

 

There is a rubber boot in the middle that is actually the duct work for you side window defrosters. This is not joined and seals by compression. Is this the one you are talking about? It is just a round tube with a flange for sealing.

 

negative, i know that opening, the one im talking about is like a hinge/arm for the door. its in the middle of the top and bottom hinges.

 

The only other thing I have on my 04 door that is rubber is the corrugated tubing that holds the power lines for windows,locks,and mirrors. I doubt if this would gert water in it, but it might be a good idea to have the dealer look at it. As it's under warranty, make them fix it.

 

i will have to get a picture posted to show you what im talking about. its the arm that holds the door open and closed.