I've done a bit of research on dark brown eggs. Since there are several chemicals that make up the dark egg pigments and there are a number of biochemical reactions that produce those pigments, it stands to reason that if the basic chemicals to make those pigments are unavailable in the diet, shell color would suffer. If they are abundant in the diet, color will be enhanced. Time in the shell gland can also affect the amount of pigment applied. Just as stress will inhibit the application of pigments.
It's possible that animal protein and the micro nutrients in fruits like pomegranate, acai and blackberries could make a difference. Those are things that won't be in chicken feed.