Just to put in my two bits...
I have been told that when removing door panels, trim or any interior items, to replace the little plastic clips that hold them. Once you have removed these clips, they almost never hold things in place properly again. I found a place on the web that sells loads of these things for a reasonable price.
Also, I had a similar problem with a Jeep Grand Cherokee, and it was the door lock arm. The doors are quite tricky and easy to put togather improperly. Just check and double check before you call it a day.