I am having a similar problem. I have a pitbull that had a litter of 6 (4 males and 2 females) The puppies seemed to be thriving and all were a good weight. The are currently 3 weeks and 2 days old. At 2 weeks I went in to the room and one of the puppies was having trouble breathing. It looked like he had the wind knocked out of him. He would let out little cries that also seemed very strained. I took him in to the vet and they said he had some contusions on his lungs and had to put him to sleep. I assumed that she stepped on him. She is deaf and isn't very aware when they are whining or anything. A couple days later I got home and 2 of them were having the same symptoms. I took them in and they were put to sleep as well. Thinking she stepped on them, I separated her from the puppies and took her in every 4 hours to feed, watching very carefully each time. A couple days later (yesterday) I woke up and one of the puppies was lifeless. He was dead. Now I am at a loss for what is actually going on. I have stopped feeding them her milk and they are on a milk replacer now. The vet and I aren't convinced that's what it is, but I am taking every precaution I can at this point. I only have 2 left and I am not satisfied with the "fading puppy syndrome", as it seems to be a blanket diagnosis for all unknown causes of death. The puppies were the first 2 and the last 2 born, so I don't think its related to the order. It could be viral or bacterial, but after reading about those dalmations I am not so sure about that either. It's very frustrating, I hope this information is a little helpful to anyone experiencing the same thing. My heart goes out to all of you and your dogs. Good luck!

Also.. here are some things I just thought of... the first one had symptoms for about 2 hours before passing and the others about the same amount of time. One of the 2 ones to die coughed up some clear fluid before passing and continuously cried, while the others didn't.

Mlashbrook, you really need to ask this as a separate question. I've reported this to the moderators so they can start a new thread for your question.

I'll see if I can help when they move it.

Did you do genetic testing before breeding? This could be genetic, which is why it's never a good idea to breed without testing both parents.

You aren't happy with fading puppy syndrome but that's what it sounds like to me.

Some things just aren't meant to be, I have seen whole litters lost to FPS through no fault of the owner.
On the other hand I have seen whole or half litters lost because the owner just simply missed a few steps.

What temperature did you have the whelping box at?

And here comes the rant - Why on earth did you breed from a dog with a genetic problem? (deafness)

mlashbrook, now I can advise you.

Do yourself and your animal a huge favor. Get the mother spayed. It sounds like the puppies were bruised during the whelping, and the contusions aren't healing. If her deafness is genetic, it can indicate other predispositions like hemophilia.