Momma keeps moving runt out of the box
 

I don't think it is that she isn't interested in her, she feeds and cleans her. But she has been [COLOR=green! important][COLOR=green! important]bedding[/COLOR][/COLOR] outside of her whelping box and trying to move the pups, well I've only caught her moving the runt. She wants to move them under the [COLOR=green! important][COLOR=green! important]bed[/COLOR][/COLOR]. (there are 3 pups) She takes her (the runt) by the tail and sets her outside the box, and then heads under the bed by herself...what is she doing??
Also, They are 2 days old as of 9 this morning...is it to earlier to clip their [COLOR=green! important][COLOR=green! important]nails[/COLOR][/COLOR]...maybe this will help????

Wow...I am not a breeder, so I have no idea. I just hope someone sees this. Poor little one. :(

Sometimes a dog will do that because they sense something is wrong with the pup

I agree.

you need to confine mom to one area, in an x pen or small area with the pups, she needs to keep them warm. if she is feeding & cleaning the little girl just make sure mom is keeping her warm also, hopefully she will accept her if not you may have to supplement her. please do not let mom wander all over with the babies. is this mom's 1st litter? if so you may have to sit with her and help her out to get use to takeing care of the babies. just let mom out long enough to potty or put a potty pad in her area with her.

Yes, she is confined to our guest bedroom it has window french doors with glass so I can see in from the living room. Her whelping box is in there, but she has taken the runt puppy out of the box, and under the guest bed 4 times now. ONce in the middle of the night I was awoken by the puppies cries (I sleep in the guest bed now)
She wouldn't go on potty the pad in the room, so we moved it out to the living room. She comes out and goes on it, and then runs around scratching and bedding in other areas of the house, even under the couch, which doesn't have much room. It makes me feel like she is trying to tell me I need to move the box to a new area. Just not sure where that would be. To drafty in the living room, and we have daddy we need to keep away as well, thus her whelping box was placed in the guest bedroom. She only seems content when I lay on the guest bed with her and the pups.
Her temp continues to be on the high side (102.4 this morning) Wonder if it is just to hot in there for her??? I just don't know why she only picks the runt to be moved. Other then that she feeds, clean and keeps the runt warm.

Your runt is fading and mama knows this. You probably need to take it to the vet . Your little runt is in trouble someehow. mama's will push them away when they are dying. if the runt gets cold and hungry there is no chance for survival unless you take it to the vet. There are several home remedies for trying to save pups on here but my vet thinks most of them are useless and that the people that have luck trying them had just that,Luck.. Since they are only three days old, take mama and all the pups to the vet with you. There might be a congential problem that the vet will find. i don't mean to scare you but unless you act fast, you will lose this pup. I also ditto what someone else said and you answered you had her in the bedroom. That is too large a space. You need the whelping box in a crate or an x-pen but even that will not save this little one. Clipping toenails has nothing to do with it.

I have to agree about the puppy not making it if you don't find out whats wrong, ie: take the whole crew to the vet asap. If she is moving it out of the area of the others then something isn't right. If it is dying then she will sense this and move it away so that she can focus on the remaining babies. I know this sounds cruel but that is just Mother Nature. Also as far as keeping Mom and babies in a small area, right now those babies need the warmth of Moms body. For the first three to four weeks after my babies are born they and Mom are place in a large carrier (german shepherd size). Mom is let out every half hour or so for potty break and to get something to eat then put right back in with her babies. The reason I use the carrier is because it is big enough for the mother to move around but not so big as to the puppies can't get close to her and stay warm. So my recommendation to you is to confine your girl in a much smaller area with her babies, she doesn't need a bedroom all to herself, and as the previous poster said if this is her first litter then you are going to have to help her out so that she can learn what she needs to do if instinct doesn't take over.

I want to jump in and give you a little hope as well. Bailey did the same thing with the runt in her first litter. she was the smallest only weighing 2 1/2oz when she was born. I also have no idea why she did it, but I would wake up multiple times during the night to a baby crying under the bed. Bailey would take her to the other side of the room and try to run back and forth to be with the other two in the whelping box and to be with the little girl. I thought it maybe was a male/ female thing LOL but I don't think so. I eventually put her in a kennel at night so she wouldnt move the little girl. That worked and she stopped doing it. The little girl is now 3lbs at 7 months and doing just fine! So, IMO try putting her in a confined area with the babies so she can't move or leave any of them.

Best of luck to you and your babies!