There shouldn't be any measurable difference between the floor of the tub and the top of the paper towels... Cypress/aspen/eco-earth on the other hand will have a big difference.
How many sheets of paper are you using? (you only need 1)
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There have been a few threads here with cases. Basically it boils down to the store had mites and they got into the bags of substrate. It certainly isn't terribly common.