This may sound silly, but does the pee of un-neutered males smell stronger/worse than females or neutered males? Since his neuter, Random's box is much less ripe...
Definitely! I have 3 males and 3 females that use the litter boxes. All have been fixed except for one male. He's getting fixed in a few days. I know when he has used the litter box just as soon as I walk in the room. Tomcat pee has a very strong smell. If they spray furniture or anything else it's almost impossible to get the smell out. That's also how they mark territory. Once my other males were neutered I didn't smell their urine.