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Could be the shavings...I've never encountered that, but anything is possible. Do you see anything crawling? Do the chicks act like they are irritated by some type of bug? Chicks at that age are a little "itchy" since they are losing down and pin feathers will be coming in, so you will see them...

Welcome To BYC I wouldn't think chicks from a hatchery would have mites/lice, but it would be good to look them over really well to see if you find any crawling bugs. Where did the dirt come from? Maybe from that? Hard to know - maybe you are allergic to the pine shavings, chicks, dirt, etc...