As I said, place the vegetable above the box rather than letting it "fall" on the surface in CK. Should fall according to gravity when the cell loads.
With respect, do you think I'd be asking for help if that worked? I tried both that
and selecting "Ignore Havock physics" (or whatever the tick box is called). They're not simply falling through furniture, they're moving position laterally. I'm working on some additions to Whiterun. The market stall there that sells veg has its veg moved to the right so the Leeks are under the box that should house the Tomatoes and the Tomatoes are one box width to the right of the Leeks. Similarly, I have a stack of Cheese on a counter in the Creation Kit but when I fire up a game the Cheese has moved laterally to the right (again) so half the stack is on the floor, the other half on a different stall. Finally the Kettle (black pot) that should be in front of the Veg counter, whilst showing in the correct location in the Creation Kit, actually has moved over to the Well. I know this isn't a problem with my save because if I deactivate the mod, everything is in the correct location.