inside the box the air pressure changes as the sub moves, when the sub goes in the air pressure goes up, when the sub goes out the air pressure goes down. It would be just the oppsite for the cabin of your car. What this means is things in your car are always expanding and contracting/ inside the box as well as out. now with that stated it simply comes down to this, the more rigid something is the less it will flex a.k.a rattle. The wood your box is made out of should very rigid, most of the sheet metal on your car is not as rigid as that. and most of the move movment comes from thing that are not sealed solid, like your trunk lid that will move up and down as the air pressure changes. Where your box should be solid enough that the only thing moving is the sub its self. which brings us to your door, deffently not a 100% solid seal, when the speakers in you room move the air the door being a week seal is a good place for the air to try and equalize its self. speaker moves out air pressure goes up door gets pushed on, speaker goes in air pressure goes down door gets pulled on, done with a rapidly moving speaker it causes the door to move in and out, or "rattle". Leave your open just a crack on a windy day and open a window, bet you can get it to close.
hope this helped and also hope all info is correct. basicly comes down to air movement vs. rigidity.