Shades on babies can be caused by a number of things, some is developement e.g. if a rat is slightly behind in terms of growing up (kind of like a runt, but not always a true runt, just not as strong as the others) then there colour lags behind the other rats, often by up to 2 or 3 days. Another is recessives, these are genes that they are carrying but not expressing. A good example of this is the red eyed dilute gene, when you have 2 copies of it the rat looks either buff (beige) or topaz (fawn) or some variation of the colour, however if you've only got one copy it actually slightly lightens the shade, so a black rat will be a paler black than one not carrying the gene, the agoutis are also warmer and brighter (some agouti breeders add it in as RED carrying agoutis often show better). This is a fairly extreme reaction for a carried recessive (it was so obvious in one of my litters that i managed to predict which agoutis carried RED and which didnt from a few days after birth) but other recessives do lighten the colours as well. I remember meeting some black essexes that carried so many hidden recessives that they were closer to a blue rat than true black.
You aslo get other genetic factors, these arent as easy to define or track, its why selective breeding works, the genetic relationship isnt simple but if you select for blacker rats then over years you will get gradually darker black rats.
Then theres dietry factors, diet, especially things like protien and copper, really affects how the coat produces its colour. It doesnt affect nursking kittens so much (unless mums under nourished) but it can hit them later on in life. Some rats fed an inappropriate diet loose loads of colour, there owner thinks they've discovered a rare variety such as chimera, feeds them well and a month later there rat is actually mink or agouti or similar.
