It might take the pumpkin a little time to do its work. How much did you give him?
He may be developing an intolerance for one of the ingredients in the food--maybe a grain or even one of the protein sources. And yes, those intolerances can develop even after a dog has been on a food for a long time.
You might want to talk to your vet about a probiotic appropriate for puppies, too--we noticed a vase improvement in our dogs' stools when we started regularly adding a probiotic.
Poor little guy! I hope you and your pup get some sleep soon!