I doubt if pine shavings caused the problems. More likely an issue with fumes and air circulation.
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We now think that it was a pan in the oven that started flaking off what could be Teflon ☠
That confirms that it is an environmental toxin killing them-- I guess that is good and badOh, to answer the question in your title post ... we also kept our chicks in plastic bins at first. We used puppy pee pads and pine chips. Easy clean up.