Hmm could be existing crates maybe not automatically closing if they were open when last saved. Does opening and closing its inventory fix it?

Playing with it a bit more, it seems that pressing E on the crate to access it opens the lid, at which point it remains open until you pick up (carry) the crate which closes it... and then you can put it back down in its closed state.
Mechanic is kinda weird, maybe not as intended, but at least I understand what its doing now.

Hmm yeah that's not intended, but I also can't reproduce the issue. For me it's working as intended and the crate closes automatically as soon as I stop interacting with its inventory.
Try crafting a new one and see if that will also not work as intended. Maybe old boxes are more broken than I thought and need to actually be replaced...

How do i pull these rods out?