What Causes Unusual And Smelly Stools?

Hi There, I am worried about my little guy. he is 16 months old and has had poop issues for over 4 weeks now. My doctor suggested a lactose intolerance and we did send his poop off for testing. Came back he had crystals in his stools and it was some kind of food poisening. He was NOT sick at all, which I find wierd. He was crampy at night time and unsettled but was happy during the day and eating and drinking. He has finally had some normal consistency stools but they are charcoal colour and greeny and are HUGE and extremely smelly still. He is still unsettled at night time and seems to have a lot of gas that he is unable to pass. I am still worried after seeing my doctor and wonder what else could be causing this? He is 23lbs and 2.5 feet......eats healthy and is active and happy.