Could be something loose inside the door and the only way to find out is to pull the panel and look.
The noise with the windows up and top up could also be friction on the weatherstripping. I didn't believe this until I tried this myself, but you do need to periodically lubricate the weatherstripping. The best thing I am aware of is Dupont Krytox GPL 205. Super expensive, but you'll be amazed how much quieter doors, windows, and the top seal get when you remove that little bit of friction.
Patrick
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