I have the same problem. Apparently my wood has begun to rot due to this issue

I've also noticed that the same is true for ammo crates. I'm not sure if it's intentional, but if it isn't I believe it's because when patching the buildings they didn't include the "<preventDeteriorationOnTop>" flag (which is present in the original) and it got overwritten.

EDIT: though looking at the defines for the shipping container it does explicitly set the aforementioned flag to false, so it seems like it's a deliberate decision to not have shipping containers protect from deterioration.