The problem with shreddings, wood chip and bark particular is that they can grow molds which when they dry, fruit and produce clouds of spores. Chickens encounter spores all the time when foraging so some exposure can't be avoided but in poorly ventilated and confined spaces it can become too concentrated and seriously damage their respiratory system. There's a nasty infection called Aspergillosis see
http://www.thepoultrysite.com/diseaseinfo/7/aspergillosis which hardwood chips are particularly prone to causing. This is why I said keep well ventillated and watch out for mold growth. Never use these materials in the house.
Disinfect the surface ocassionally with a dry powder disinfectant or an Iodine based one (Vanodine V18).
With shreddings make sure they are well rotted and don't contain anything poisonous like YEW.
It's autumn too so don't waste those free leaves on the bonfire or compost they make excellent run coverings as does dry bracken but not straw which harbour a very itchy mite (not Red Mite) and also becomes very smelly and insanitary when wet.
If your wet runs persist see your doctor
HF