Cedar (and to a lesser extent, pine) contain phenols that can cause respiratory problems. Studies have shown that they cause changes to liver function (the ones linked in this article are on small animals, but I think I remember reading about people working in the lumber industry having similar liver changes)why is cedar toxic to chickens?
I imagine the old cedar chips that have been airing out for a year are probably past the point of being a significant threat. But I personally wouldn't use fresh cedar as bedding, even in a run.