I used to have this with some of my litters... I'm not certain what it was, but my guess is that it may have been coming from a dirty nestbox. Are your babies still in the nest? If they are still using the nestbox, have you ever cleaned out the entire nest and replaced it with fresh hay/bedding?
With current litters I try to clean out the nestbox at 9 days and then again at 14 days. (Depending on your litter size this may need to be done more often. I usually have no more than 4 kits in a litter.) When they are at 14 days, I either remove the nestbox completely or tip it on its side for another week.
I think for my rabbits, when the bedding in the nest was left too long and became dirty they began getting this "dandruff" or white flakes in their fur. Although, it has been a long time since I have had this issue, and I may have had some litters that got it even with a cleaner nest.