I would take him to the vet to be checked out if I were you to see what's causing the problem.
You might try changing his food. My girl kitty could clear out a room when she was little- she was sooo stinky. I changed her food and discovered it was one specific variety of beef flavored can food. She has not been near as stinky since, but every once in a while something gets her going.
Did your vet give you any info at all on what this could be? Where all his tests normal? The simplest answer is diet. If there's blood...it could be a minor recurring infection. Otherwise, this kind of thing is usually a sign of digestive issues. You may want to try a "bland kitty diet", something high in carb/protein with no additives or other chemicals.
Thanks for this help - I'll take him to the vet on Monday to be checked out - and have already changed his food (which seems to be helping). Thanks again - I'll let you know how the vet goes :)
Did you find out what this was? I had a similar problem when my cat was a kitten and he had worms. He was very smelly, runny stool, and his anal area would bleed after going to the bathroom.