The problem was the cleaner.

Cat pee, if not cleaned properly, has a half-life of six years, and there's a component of cat pee that "regular" cleaners are not chemically capable of removing - and that's what keeps smelling. All you need is a good enzyme cleaner, like Nok Out, Urine Off, Stink Free or Anti-Icky Poo.

Here's an article that explains why, and how to use them:
http://www.thecatsite.com/a/how-to-remove-cat-urine
Given the spots were already cleaned in a way that just helps "set" the problem, you may have to clean several times with an enzyme cleaner.
You can find all the cat pee spots by using a black light at night.

All of that said.. given that they had adjusted to each other without anyone "marking," I'm concerned that someone has developed either a bladder infection, a urinary tract infection, idiopathic cystitis, or is just doing their best to let you know they're in pain from something like a bad tooth - or other medical problem. Cats will and do pee outside of the box for stress-related or territorial reasons. But USUALLY it is for medical reasons. They have very few other ways to let us know there is a problem. Can you set up a webcam to see which cat - if it's just one - that is doing this? (Of course, once the scent of pee is outside the box, it can then encourage the other to pee there... that's why the main solution to peeing outside the litter box is properly cleaning up the pee).
But given peeing outside the box is so often a medical problem, I'd try to figure out if it's just one cat, and then get that kitty to a vet asap. If it is pain (and bladder infections are pretty darn painful), that's a real problem.

And if it's the male cat, if the problem is caused by crystals in his urine or sloughing of his bladder wall, he can become blocked. Not to scare you, because obviously if it is him, he certainly hasn't completely blocked yet, but a complete blockage will result in death within 24 - 48 hours.