How high off the ground are your stands? Are you using a solid bottom board or open mesh bottom board? You said that you have re-queened, was it with a queen from a different line of bees? Have you tried, as a last resort, removing and giving all the brood to one colony and then shaking the adult bees onto foundation? What have your weather conditions been? These are the questions I was taught to answer when faced with chalk brood disease.
Try using stands that lift the hive 8 to 12 inches off the ground, if you are using open mesh bottoms close them during the cool, damp part of the day (if any), do a shake down of the adults onto foundation and feed, if the new queen was from the same queen line as the one you replaced, try to find a queen from hygienic stock. Chalk brood usually infects brood that has been chilled during the first 24-48 hours after the egg hatches and the adult bees don't keep the young larvae as warm as they should. The comb can hold spores, so I would try a shake down on one colony and see if it has an affect.