We have this problem at our clinic with the clinic cats. Two males, both are neutered, both have several litterboxes that they use, but they will occasionally spray certain areas. We think it is a territorial thing with them because it's their home, but there are hundreds of different cats and dogs that come in and out of the clinic every week.
In a home environment, it may be that he was neutered later than usual and so the marking is a habit. Are there any other cats in the house? That would make it a territorial thing, unfortunately it is very hard to stop. Are there stray cats outside? I know of a family who had trouble with their male cat marking its territory inside the house because it smelled stray cats outside.
Of course, that's a real challenge to keep the strays away...
They used traps to catch 'em and took them to the shelter.
The only thing I know that occasionally works is to scrub the heck out of the walls that he marks, and use something like nature's miracle or another good enzyme-based cleaner to try to eliminate his scent. It's a pain, but trying to move some furniture around, if possible, to physically block his access to those specific areas sometimes can distract the cat, except for those determined ones who pick a different place.
If at all possible, keep an eye on him when you're home, and use a water bottle to give him a good squirt when you see him with his butt to the wall. When everyone is gone, try putting him in a small room with his litterbox, food, water etc. to prevent the marking or at least limit the area he can reach.