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.  :)