My name is ***** ***** I’ve been involved professionally with dogs in the health and behavioral fields for over 18 years. My experience is with both vet care field and breeding. It will be my pleasure to work with you today.
It sounds like you have treated for the most common causes of loose stools such as coccidia, giardia, and worms. I'm pretty sure you have probably already done a fecal check at the vet as well. If not, you do want to do that.
One cause could be herpes infections though I would expect other symptoms such as weak suckling, crying, painful abdomen which it doesn't seem is present. They would also have to contract herpes late as when contracted early the pups usually don't make it as I'm sure you know.
One thing that could be the cause especially if any of the parents are from the same bloodlines is an allergy condition. An allergy could affect a whole litter or more of puppies. So you might try some benadryl at a dosage of 1mg per pound every 8 hours and see if the stool firms up. If so you might have to experiment with different foods to see which ingredient might be to blame.
Another possibility is that your water supply is contaminated with a protozoan infection. Treating the pups would not be effective if they were contracting it on a regular basis from the water. We have our well tested regularly to prevent this but also flush our pipes with a mild bleach solution overnight to kill any bacteria, etc that might be in the water system. Other animals in the kennel might have developed an immunity to the bacteria or infection and other litters may have had immunity from their mother as well.
I hope this information is helpful to you. If you would like any additional information or have more questions please don’t hesitate to press the reply to expert or continue conversation button so I can address any issues you still have . If you do find this helpful, please take this opportunity to rate my answer.