I'm betting your kitten is suffering from a single celled parasite that causes diarrhea. In all likelihood, it's giardia, coccidia or camphyobactor. Call your vet and ask if they can try your boy on Metronizadole (flagyl) for 2 weeks (3 is even better, but if his stool firms up after a week, then tell the vet you want to continue for a full 21 days of treatment to make sure the problem is completely gone). Many times, these parasites do not show up in routine stool samples, and just trying the treatment for them is the easiest and most effective way to eliminate the problem. Once his tummy feels better, I'm 99% certain he will start going back in the box for you. You can try a litter called Cat Attract Cat Litter, but it won't be much help as long as he is hurting.
Please let me know how things progress with your boy. Note that he may drool excessively and even foam at the the mouth with this medication, but make sure you stay the course and get it in him at all costs. The further back in his mouth the better so he tastes it less. Don't try putting it in his food as he won't eat.