Just to be on the safe side give it a try. Load a savegame you made before you started working on your mod and go to the cell where the crate is.
And it is not a vanilla crate that existed in the original game? You've made a new form and dragged the crate into the render window, right?
Yes, a few days ago when I first began working on this I made a new form from a vanilla crate and dragged it into the space, and positioned it where I liked it at the time. Then, after playing for a while, I decided I needed to add some more containers, so I moved the original one down off a cupboard it was sitting on to the floor. It's still sitting on the cupboard in the game even though it's clearly sitting on the floor in the CS. Unfortunately, I don't have a save that far back any longer, lol. I had to clean them up and deleted probably 100 or more of my old saves.
EDIT: I think I have a work around for the save..brb, lol.
OK, thankfully, I had a save from inside the sewers when you start, so I loaded it up and coc into the cell and all is as it should be. But, that still begs the question of why in the heck it isin't moving to where it should be moving to in the older saves? That's really strange to me because that would mean that you couldn't work on a mod as you play along and benefit from your tweaks as you play without having to go way back to before you were in the cell? :shrug: