How old is your puppy and how many food changes has he gone through and in what span of time? Too many changes will cause irritation in the GI tract and therefore you will continually have stool problems because of the irritation. My suggestion is to stick to 1 food for a good amount of time, use a probiotic (I prefer Forti-Flora - available at your vets office).
If after a period of say 6 weeks you are still having stool problems - then consider switching the food again (I actually prefer to wait closer to 3 months, but Loki was very fussy/sensitive to food). Also ensure you rule out anything medical going on by getting a fecal done.