Some hens will brood on absolutely nothing at all, even empty air. The clutch doesn't have to be theirs or even physically present, if they're convinced they should sit anyhow.
Glad that worked but not sure how the other birds are supposed to lay, unless you're saying only she needs the large boxes? Hopefully it was enough disruption to stick.
A cage really isn't a form of torture - it disrupts them from the nest (which is what you were doing with the rocks) and if you have it elevated it allows for cooler air to get under them to cool off their bellies. To me it's worse having them sit for weeks losing body condition without anything to show for their efforts.