Hi B.,
I am a veterinary technician, and just to let you know you're not alone. Kitties can be very picky and difficult when it comes to their litterboxes. As long as you've had him checked for intestinal parasites, a urinary tract infection, or anything else medical (exam and bloodwork) it's probably behavioral. Some things you can try: try a new kind of litter-if you use clumping, try regular litter or vice-versa some kitties are particular about the substrate they go on. Try a different kind of litterbox-maybe a covered one for more privacy, or a larger one? Try a different location for his preferred litterbox if you can. Also, pay attention to whether the other cats are leaving him alone when he uses the litterbox (I know-can be difficult, I have 3 cats of my own!).
Some other ideas-is he getting enough attention? I know my cats just don't get the attention they used to before my daughter was born.
Did it start around the time your son was born? Sometimes kitties will start w/ inappropriate elimination when something in their life changes, like a new baby. On the bright side, at least he's doing it next to the litterbox, instead of somewhere else in the house...
Those are all the suggestions I can think of right now. Good luck with your kitty-I hope something works!
A.