I don't think either of those two would be irritating. If it was red cedar or pine that wasn't kiln dried, I could see issues cropping up.

A hamster I kept had spontaneous fur loss on her back. It was very odd, and since she was a pet, she was taken to a vet who had experience with rodents. He suggested that she could have a fatty acid deficiency, which can lead to hair loss. She was given a few drops of cod liver oil on a graham cracker three times a week, and it cleared up. While it is less likely, it could be because of a nutrient deficiency.

The other reasons could be diet related still, such as an food allergy or excess protein (which can lead to hair loss in rats and mice). Studies have shown allergies can be genetic, though the parents aren't exhibiting symptoms, and you have such a wide pool of breeders. In mice and rats though, wheat is a common allergen, and the vita rat mix has plenty of it. But the lab block should provide adequate nutrition since it is designed to be complete.

Wish I could be more helpful than just adding possible theories. I've kept rodents for many years, but only once have encountered a skin problem (if the aforementioned hamster).