Since parasite tests came back negative, I'm practically sure it's the food. We went through loose poop period with Moses and to find a mix that suites him seemed to take forever.
Very, very slow transition with puppies though. Moses was on Science Hill when be picked him up. We immediately started to transfer him to Grain Free Orijen Puppy.
His poop varied throughout puppy period and early adolescence...loose yellowish, loose yellow/brown etc. on rare occasions he pooped truly solid dark brown. I also noticed a correlation with heavy exercise and good solid poop (when he was a bit older).
Note also that if the poop is loose for a good period of time, you should check the anal glands. Normal solid poop cleans the glands, but loose stool might also cause anal glands to fill up.
Orijen is a good food but high on protein. Later on we learnt that it might cause some issues with some dogs. I believe that was it in our case. In any case if/when I'm going to get another puppy. I will start with Orijen Puppy, grain free. Other good ones are Acana Puppy and many here give Fromm with excellent experiences.