I have had similiar problems each year and I finally figured out what the problem was. My pen is outdoors and has a pig house with four enclosed sides and two doors that are open all the time. Each year when the pigs come in they would get a cough and I would be worried about them. This year same thing happened. When I had to move a female out to another pen because she had a prolapse . As soon as she was there (Which was a more open to airflow) she stopped coughing in 2 days. When I finally moved her back to the other pen she started coughing again. Last weekend when the pigs were in the house moving around I could see some dust from straw and dirt floor so I pulled a board off the sided of the house to allow more air flow and hosed down the dirt. In two days the cough was gone in all the pigs and they are running around. To me it did not seem like I had a bad dust problem but you may want to make sure you have some fans working help air flow to be sure. Hope my theory works for you but I don't know what your pen situation is.....Good luck.