Hi
For what it's worth, I have two hens and two boxes. They take turns in the box furthest from the little window. This winter, I added hay on top of the boxes for insulation, and they made two nests up there, too. They poop in the one on the window side and occasionally lay an egg on the other side now that its warmer and they are back to using the "bottom bunk". All winter, they laid their eggs in the "top bunk". Is there anything near the other boxes that they don't use that would make those locations less desirable? Maybe there is less headroom above the nest that your hens fight over. I think they like to feel enclosed. Or at least mine do. I let my chicks out the other day, and they stayed under the wheelbarrow, convinced that the world was just way too big.
Based on where I saw the poop in the other "top bunk" nest, and based on watching the new chicks roost on the edge of their dishpan/nest, I'd guess that you hens are poopin' while their roostin'? Sounds like you're okay with it.