I was aware of this problem from other posts on this and other sites. My drivers door starting making a popping noise about one year ago and I thought it was due to the point of attachment of the door check to the frame. I always take my van to the dealer for all service and oil changes and I was surprised when the noise continued.
This door also had an additional problem where the sleeve in the upper hinge had disintegrated allowing the door to "sag". This happened about two years ago. This was annoying so one day I went to the dealers body shop to see how much it would be to change the hinges. Well the young guy tells me I have a problem with the door check and that's covered by Toyota. He told me they replace the door. He told me he has never had a door replacement refused. A week later I stop by to see if he's received a reply from Toyota. He tells me the replacement ends at 5 years and 150,000 km. My van is 5 years and 3 months old and has 155K km. I am waiting to see if they will contribute to the work as "goodwill". I can't believe they won't automatically do the work.
So if you have a noise in a front door that is unusual go to the dealer immediately.