Check the door frame. Its held on by the two black knobs on top of the roll bar.

I noticed mine were loose. They were the source of an annoying rattle that I had only when the top was down.

The frame moved around a bit with the knobs loose. Maybe yours is loose and keeping the door from sealing properly.

This is just a guess

 

Just wanted to let everyone know...

I put some heavy duty black tape on the door stricker/catch thingy... WTF ever you call it.

No more squeak.

Yes...I just taped up a $30 thousand some odd dollar vehicle with 3,000 some miles on it. What will I be taping up when I get 30,000 miles?

Oh well...still lovin the JK.

 

Mine has the same door noise with only 3500 miles on it. I have been too lazy to apply the black tape, so for now I just expect to hear the clunk. I also had the clutch squeak that I did fix by bending away the heat shield. The door clunk does not bother me so much, but that clutch squeak just had to go.