It's no fun dealing with diarrhea in a puppy (believe me, I've been there ... Lucky had awful colitis as a puppy ...). He recently had some kinda tummy trouble. Stool tested negative for Giardia, but one thing the vet told me might help you.
She said Giardia can be hard to get rid of and often recurs ... it can be really frustrating but one thing you can do to help prevent a recurrance is giving frequent "butt baths" in addition to the meds. The butt baths help because the Giardia is sticky and will stick around down there and as you probably have figured dogs like to lick themselves. The butt bath helps to keep him clean and prevent them from getting reinfected.
Hope that helps some and the disinfecting is a good idea. Hopefully it'll be all gone soon.
(a.k.a. Lucky's & Sparky's mom!)