I think being boxed in just made her panic - and since she could stick her head out she likely figured if she just worked at it she could get out.
*Might* want to see if you can rig up something that's wire mesh instead, so she can't poke her head out but can easily see out... I know there's...
When you manually put them in the nest boxes, do you just plop them in there or keep them inside?
When I had similar issues, when the bird went to their preferred spot to lay, I'd go and pick them up, stick them in a nest box, and barricade them in using my arms to cover the exit. 30-60 seconds...