as this is her first litter she has to learn what to do with the babies, she could have killed some of them unfortunately by accident by squashing them or bieng generally clumbsy and not knowing what she should do with them... keep an eye on her to make sure she is feeding the babies, i would get the vet to have a look at her anyway,
as it is her first litter then maybe wait for 2 to 3 weeks before handling any of the babies as she may feel you are a threat to them and kill the rest of the babies..
most guinea pigs do make good mothers.. my advice would be just keep her calm and dont mess about in the cage any more often than you have to,
you dont say if she is indoor or outdoor but if outdoor or a bit cool in your house the chill could have killed the young pups, keep her warm and add extra bedding in her cage and she will need a lot more food from now on to keep her energy up,
good luck with her and let us know how the pups go
katie