Not an expert on breeding but please keep us unformed, the hand feeding may be the only way forward. I have seen this in lambs and have participated in bottle feeding. In that case the mother sheep never took care of the babies in any way. They were not my animals, but I understand it happens with otherwise healthy mothers for sheep... first time I have heard of it for dogs. I can only assume the nipples are painful for some reason, surely the Vet has some idea.
Glad she has been checked by the Vet and can assume there is no sign of mastitis. Actually, have seen dogs that reject puppies but they usually won't clean them either. Will she let them nurse if you lay by her and hold her down? I have cleaned pups with a cotton ball and smeared it on the Mom's nose and front legs so she would lick it off and that usually works to help them accept the pups but you say she is cleaning them. She must be getting engorged if they are not nursing. Check each test to see if they feel hot. Take something white and express some milk from each teat and look at the color. See if you notice any blood, pus or green discharge. If so, she may have an infection and is sore.