Answer

My feeling is the dogs feel obliged to teach you new medical information all the time - not that you want them to just that they manage to do it!

You might have your vet check for a herpes virus titer in your adult female dogs. This can be hidden in the dams and impact the pups. You can read about herpes virus and puppy eyes here

http://www.iovs.org/cgi/reprint/15/4/267.pdf

and more info (in less scientific jargon for breeders) here on this virus

http://www.showdogsupersite.com/kenlclub/breedvet/vhr2.html

and how it impacts adult dogs and pups.

You might check your carpet source as its possible if this is new carpet that there is a chemical on it that is the problem. I know they use insecticides and preservatives on carpet for shipping. Washing carpet sections before using might work.

I can tell you I ususally change bedding twice a day washing it and bleaching and letting it air out of bleach before reusing it. (Yes obsessive I know!) I also trim puppy toenails as those sharp little nails can push into eyelids and cause infection under the lids so the eyes are blind before the lids ever open for the first time.

I'd scrub out whelping areas before use with 1 part bleach to 30 parts water as that will kill many types of bacteria and viruses.

I forgot to ask if this happens after a vaccine is given or a wormer and either of those can impact the pup's eye development.

Hope this helps you!