I filled each box with a foot of wood shavings. I almost lost two of my dogs. Both had the habit of keeping and chewing their bones in their box, rather than the open area of the inside part of the run. Both had ingested wood chips that had gotten stuck in their digestive systems. Now I put loose straw in every winter and it works just fine.
Straw is a better bedding for box stalls.
It may stick to the bitch, but the pups don't suck it into their systems and it can be passed even if the pups ingest some. It may seem that it gets wetter, faster, but it just shows more and the portion where the bitch lays should be changed each day anyway. Some use the fake sheepskin throws or pads. They are nice and soft, but check the tag to see if they can be bleached. White cotton sheets work well also.