Try to get the probiotic Protegrity. It kills allot of the pathogens that cause diarrhea. It is a chew. I use a nutmeg grater to make it a powder. It turns diarrhea around in 24 hours. It's a WOW product. Available from Vets and from willowtreenaturals .

Stop the yogurt! This alone can cause your issues. Wash the puppies using a 50/50 solution of Dawn dishwashing liquid (original blue). Fortiflora has more than just probiotics in it, another probiotic only supplement would be better and don't overdue it, too much can cause diarrhea. Feed the ID and medicate for coccidia. Good Luck!

We had more stool samples tested yesterday. Again the vet found nothing. No worm, no parasites, no nothing.
So the vet decided to dose the pups up with Ponazuril, Flagyl and drontal to see if anything has any effect. I have bathed them using blue dawn and scrubbed, and scrubbed the puppy area. I am even staying up all night with them so I can clean up as soon as they poop.
Today, some are firm, sadly though, some still have the puddle poops.

Has your Vet ruled out Campylobacter?

Try Ponazuril for 2 days for coccidia and flagyl for 10 days for giardia. You can treat both at the same time. Many, many times coccidia and giardia do not show up in stool samples and vets go in another direction because they rely on test results. I have found that these two drugs always work.

We had a litter a while ago with cows milk allergy. He couldn't eat yogurt cheese or milk. This could be your problem.

If they are negative for coccidia and giardias this is what I have tried. I boil white rice one cup dry to two cups liquid low sodium chicken broth. Adjust to your puppies. I buy plain Pedialyte and mix with some chicken broth for them to drink. We have also used the canned pumpkin.

If it is still loose I have used the old time remedy of boiling five or six cloves down in water and giving them each a dropper with some of the cooled liquid.

receipe for more sleep.

to keep our puppies clean when they are about 5-6 weeks. we put up a childrens pool, and put pine chips in the pool, and an ex pen around the pool. when the puppies go to the bathroom, it does not make a big mess, and it keeps the puppies cleaner, and you can sleep.

the next morning, we change the pool out, and use a fresh clean pool, and pine chips, and change it out again when needed. you can get the pools at walmart and k-mart in the summer time.

at the same time, the puppies get a new environment, coccodia is in the earth, i believe it takes very HOT water to kill it.

this can give you time to clean the area where the puppies, and mom have been living, and rince with boiling hot water,

My guess is it was Coccidia as the Ponazuril firmed some of the stool.

At this point, I'd give Peptobismol at .5ml per pound of pup weight to firm stool. I'd give it before bedtime and again 12 hours later. Pups' intestinal flora has taken a beating. Even excess probiotics add to the diarrhea. Pepto will firm stool until all is in balance again.

I've dealt with this situation too many times. My pups go outside for socialization periods at 5 weeks. Coccidia is in bird poop, rabbit waste, etc. It rarely shows on stool tests. I now give DiMethox (liquid Albon) in pups' water at 5 weeks for a week, then again at 7 weeks old for a week. I've never had the issue since starting the DiMethox.(Dosing on this forum and online.)

Coccidia is species specific, a dog doesn't get coccidia from bird or rabbit poop! Dogs get coccidia from dog feces or anything contaminated with dog feces or by eating a rodent (not their poop) that picked up coccidia incidentally. It's slso possible for your dog to get coccidia from eating a fly or insect that mechanically picked up coccidia. The most common way puppies pick it up is from the mother in the whelping box and it can show up at 2 weeks of age or later when the pup is stressed. Cleanliness and reducing stress can help prevent the disease.

I had a litter like this. There was nothing in the multiple fecal and there was no evidence of it being a virus. I had the pet families waiting to get the puppies and as soon as they were good enough, I let the local ones go with a big warning to the new owners. As soon as they were out of the environment they got 100% better and never went back to be sick again. With that, I let the ones that were still having puddles, and they got over it as soon as they were in their new homes. I have not have the same problem ever again. It was just that one 10 puppies litter. A total nightmare.

WRONG!! Michigan State University College of Veterinary Science has done extensive research on this. Pups absolutely DO get coccidia from other animals' waste!

MSU Link? My vet says from dog poo.

Merck manual lists various species of coccidia protozoans. Some can infect dogs and cats, with rodents as intermediate hosts, apparently. If the rodents are intermediate hosts, can't their scat pass it to the dogs? How, if not by poop, do rodents pass it to carnivores--in muscle? or in intestines, which of course have poop? I wonder if OP also has cats on the property, her own or ferals?
http://www.merckmanuals.com/vet/digestive_system/coccidiosis/coccidiosis_of_cats_and_dogs.html

"Hammondia has an obligatory 2-host life cycle with cats or dogs as final hosts and rodents or ruminants as intermediate hosts, respectively. Hammondia oocysts are indistinguishable from those of Toxoplasma and Besnoitia but are nonpathogenic in either host. (see also Besnoitiosis, see Sarcocystosis, and see Toxoplasmosis.)

"The most common coccidia of cats and dogs are Isospora. Some Isospora spp of cats and dogs can facultatively infect other mammals and produce in various organs an encysted form that is infective for the cat or dog. Two species infect cats: I felis and I rivolta; both can be identified easily by oocyst size and shape. Almost every cat eventually becomes infected with I felis. Four species infect dogs: I canis, I ohioensis, I burrowsi, and I neorivolta. In dogs, only I canis can be identified by the oocyst structure; the other 3 Isospora overlap in dimensions and can be differentiated only by endogenous developmental characteristics."

Note that insects are also listed as needing control to control the protozoan. Flies are nasty!