Ayam Cemani may very well be Birchen at the E locus and to make them full black they need some melanizers, Birchen females with a few or that are heterozygous for the melanizers can be solid black or have a few silver feathers on the top(not the body) so I believe your birds are lacking the melanizers to make them full black.
Once they are lost you can't regain them unless you introduce a solid black bird to your breeding program