Agreed that it does subside or at least become more controlled with maturity. I do shavings as a base layer to the whole nest floor then a layer of nice grass hay on top of that, putting a little "dish" to the hay layer when I am freshening it.
It's natural nesting behavior - so it isn't really something to stop, but rather something to manage from a design perspective so they can have their natural behavior but the nesting materiel stays in the nest -- if you post some photos of your nest boxes we can better advise how you might...