I have fostered countless litters of puppies for our local humane society. Most come to us from less than ideal circumstances. If they don't have intestinal problems before we get them, they usually do after a couple of days of being on a different (better) diet. I keep a BIG bottle of Flagyl handy at all times, and for normal GI difficulties, it works wonders - you should notice a real firming up of the stool within 48 - 72 hours. Now, for specific intestinal disorders like coccidian (sp?), you will need a course of Albon.
Give the Flagyl a couple of days, feed the puppy his normal diet, and I think you will see a big difference. Mary and the girls, Laurel and Bailey (and Kelsie, the last of a litter of 11 abandoned pups who will hopefully be finding a forever home at our adoption tomorrow) Fayettevile, Ga