What kind of litter are you using? He may not like the feel of it on his paws. I have that problem with a couple of mine so I have several kinds of litter in boxes. Twicket likes Yesterday's News. Ivy likes the plastic pellets. Boots likes non-clumping clay. Felicia likes wood pellets and everyone else uses the boxes with clumping litter in them! When Pete was having all his urinary tract troubles, he would only pee on shredded newspaper, so that's what he got in his box!

It's a hassle buying so many different kinds, but it keeps the pee in the box! Might be worth trying a different litter.