Honestly it sounds like a vet visit might be in order. It sounds like your husbandry is good, so he might have something like parasites going on. If you can, get a fecal sample to bring to the vet. And I would switch him to paper towels for now, just because it's easier to monitor the health of an animal when it's on pure white. Where do you get your landscaping mulch? I wonder if the mulch perhaps is the cause of your shed issue.