Over feeding any food, but especially a quality food, can cause the runs. I only use the feeding scale they give as a basic guideline. I have never yet actually fed my dogs as much as they suggest.
It can often take a while to see a real difference when you change food. I found my dogs did not do well on very high protein diets. It gave them the runs, so if you're using one that's really high (40+) you may want to look at a lower protein. My dogs are older though, so they really don't need that much.
I also swear by the 100% pure pumpkin, but that said, I would be cautious of using it to mask something. Have you had your vet rule out IBD, or some other gastro issues? Good luck with your pup. Do we have pics somewhere??