If you can I would take a couple to a vet and have blood drawn to see if it is some kind of contagious chronic respiratory disease (at least that way you would know what you are dealing with if you have not done this already). It could be all of the rain. I put shipping pallets in my coop when we have bad rains to keep the girls up and dry, that may help and you can usually grab them by dumpsters for free. I also put a lot of large pine nuggets in the coop to help with flooding.
What are you giving them? Tylan 50 is best but I firmly believe when you medicate your flock you make them more susceptible to sickness so be careful medicating them.
Remember chickens do not get colds, they get respiratory diseases that are almost always highly contagious and makes them carriers for the disease for life once recovered.
Good luck
