I've never understood this either. Storm is my best litterbox user because he always covers up his stuff and any of the other cats that leave theirs uncovered. Sunny and Cirrus will usually cover up their stuff but sometimes they're in such a hurry that they just leave it uncovered. Sky will usually cover up his stuff but will dig and dig on the door opening of the litterbox. He's the noisest litterbox user I've ever had.

It may also have something to do with the type of litter that you're using. I've tried many kinds of litter and mine have always preferred the clumping type of litter and will usually cover up if I use this kind. Good luck. I hope you're able to solve the problem soon.