I know that when I was using the feline pine in one litterbox and the scoopable litter in the other litterbox, that my cats preffered the scoopable litter. Maybe one of your cats also prefers the scoopable litter or maybe they just think it's not clean enough for them.

I think you should try putting some scoopable litter in some of the litterboxes and continue using the feline pine in the rest and see what happens. Good luck. I sure hope it's not a behavioral or health problem.