There is your problem having babies with such a difference in age means the bigger one get to eat while the other do not some may survive at times but if you breed for food you really want to put females together that have the same size litter.
You also want to remove the male as well.
Having the female birthing individually is really ideal, especially when the skin of the babies is so fragile during the first 5 to 7 days.
Also try to avoid harem breeding if this is what you do with rats it takes it's toll fast when they are pregnant and nursing at the same time a good rotation is better not only for the female but also the babies.
Finally get ready to replace your female soon.