Young stray mom ignoring week old kittens

We have been feeding and loving a stray 9 month old when she gave birth a week ago. She originally had 5 babies, 1 passed at birth, and 2 had to be put down by the vet due to an extremely traumatic birth(4 were fused together by their umbilical cord) so we came home with mommy and 2 precious babies. Originally mom was doing excellent nursing and taking care of babies in a little "cat house" my husband made. This morning she moved 1 baby into a box on the porch, leaving the other one alone(he does have a slight disability in his leg from the fusion at birth) eventually she did move the other one into the box but now she seems to b ignoring them both! Doesn't want to go in the box with them, and won't let them nurse. Please help, we are not experienced cat owners, and I certainly don't want those babies to not get what they need to b healthy. DR said not to force her to be with the babies but I am very concerned abt their well being. I just don't understand why after a week she has now seemingly rejected them both. I am a very concerned grandma and I'm hoping that someone can help

Can you bring them inside and put them in a room together with food, water and a litter box?  It will be harder for her to ignore them if she is in a room with them.

Are the babies crying?  She may be feeding them, and then stretching her legs while they sleep.  If the babies are crying, and she isn't wanting to nurse, can you check and see if her nipples may be swollen or if the skin is irritated? Cats can get mastitis which is very painful and she may not nurse with that going on, or if the skin is very irritated it could be unpleasant to nurse the babies and she might avoid doing it. If here nipples are hard and swollen, you can try warm compresses, and gentle massage to get things flowing again and hopefully prevent infection.  If they are hard, swollen and feverish, she may already have an infection and could require vet care.  If the skin is irritated - hmmm, not sure exactly what - but you can use ointment to soothe the skin and maybe she will get back to nursing. 

Good luck.

If the nipples are irritated you can put some olive or veggie oil on them.  Udder Balm is very good as well.  Ointments may have toxic ingredients.

The 3 of them are actually in our enclosed porch, bc we live in Florida and it's still rather warm. Mommy's food, water, and a litter box are all in the enclosure as well. We have left them in the box that she moved them too, but unlike the first week, she almost seems uninterested in them

Her nipples seem to be okay she just seems really uninterested in them, in fact she kind of growled a little bit when I tried to coax her into the box. I was wondering if she is rejecting them bc one has a tiny wound on her belly from the umbilical cord. They had to be surgically separated from each other bc of an anomaly with the cord at birth. I'm just concerned she seems very lethargic and uninterested

If she is lethargic I would take her to the vet.  this doesn't sound right.

Pick up some KMR as well in case you need to feed the kittens.  Get some 1 -2 ml needleless syringes as well.

If you have a kitchen scale you can also weigh the babies to see if they are gaining or losing. If they are sleeping and not crying, they might be alright.  If she senses you are watching or paying too much attention, she may be avoiding the box while you are around to keep your attention away from the babies.  Of course you will know more than any of us who haven't seen momma or babies, since we can't really gauge how she is doing from posts.  Having kittens is a big ordeal - and she is a new mom... Just keep an eye on them and try not to worry too much... and good to have the KMR on hand, but if momma is feeding them, best to let her continue.  If you are feeding them every two hours, they won't be hungry to eat from mom.  Please keep us posted. Having babies is soo exciting.   Did the vet feel the kittens would have any issues as a result of the birth issues?