Hi, Nathalie, I am not an expert in this area but I'll nutshell a problem I had and maybe something will help you find what is bothering your puppies.
Got a puppy mill rescue dog, who was vomiting and had pudding-poo. After trial and error went to a second vet who diagnosed whip-worms because by this time my dog got it too. Rescue boy was so infected he developed a secondary lung infection. Since it was taking many doses, because it's hit or miss with the timing of parasite life cycle, also used DE in diet. Remember, any parasite is infecting the other animals, as well as the location where they do their business, so clean up after each 'deposit' and spread DE over whatever remains you can't pick up, make sure you don't inhale while spreading it. The vet/s thought he had a secondary parasitic infection, which was thought to be fleas, although there were no signs. All they need to do is scratch one flea off them, swallow, and now there's a new parasitic infection. Again, he needed many treatments. My dog didn't, but the vet said she should have them so avoid getting reinfected. Ended changing food and adding yogurt & probiotic and he slowly got better but it took months. Two items that may help you: The stool was checked several times and no parasite. What finally helped was when they gave me several bottles to collect specimens. I took some and left it outside for a day or two, and viola, they were there. (It was warm outside). Looking back I should have also slipped a probiotic into his behind after the parasite was gone. Hope you find your answer!! Cindy p.s. I kept him. :)