Giardia!
I have never been so thrilled in my life to hear "your pup tested + for giardia" before in my life!
we've been to heck and back with this diarrhea. He had crazy loose stools, was put on a bland diet, pedialyte, and pepto. I called the vet after 3 days of loose stools and asked if we should run a fecal. They said yes, bring in a sample. Well from then on out he had solid stools, so we figured maybe he's just sensitive.
He was on a slow transition to real kibble and we did a 6% increase in kibble and were back to violent, explosive water diarrhea. So i called the vet again and said we were going to bring in a sample for real this time.
Just got the results. On 1 hand i feel bad for not just taking it in sooner, but on the other i do find it weird that his stools show improvement each time i call the vet... hmmm does he know?
Just throwing it out there to all you with puppies with poopie trouble that a proper fecal can give you lots of peace of mind.
Actually, I know just how you feel. Our dog had giardia and it took 2 fecals to get it diagnosed the first time. She went through two rounds of meds, then was back to normal. Then 6-8 weeks later she would show symptons again, but the fecals didn't show anything. So on to endless food trials. To find out 4-6 weeks later...giardia again. So frustrating. We never really knew if it was giardia, IBD or an allergy. She just kept exhibiting symptons that could have been any one of those things. Spent almost three years dealing with it. Then moved cross country, switched to a prescription diet and she's only been sick 2 times in 11 months, a record for her. At least with a diagnosis of giardia, you know how to deal with it. 
