I have my chicks on a double thickness of paper towels over top the pine shavings. I did that just to make it easier for them to move about as I was afraid the cardboard under the shavings would be slick plus it keeps them from eating the shavings. Maybe the shavings are giving off dust or fumes as was mentioned above. Try some paper towels on top and see if that makes a difference as I'd think the paper towels would prevent the fumes/dust from rising up as badly.
Just a thought.
Just a thought.