I don't think it would be the shavings, possibly mold and mildue if they were not changed regularly, I use barley straw in my fawn barn for bedding, and the amonia from the urine gets nasty after a three or four days the uric acid fumes hover near the floor because of the weight of the gas and the barn didn't smell real bad unless you got into fawn sleeping distance , to clean I use diluted chlorine bleach and a fine push broom to scrub the concrete floor . Has anyone ever put lime down on the floor before the bedding?