Do the silkies "share" all things in common with your healthy birds? Meaning, same feed, same water source, housing, etc?
Is there any way to talk to the breeder to ask if they are having any problems with their lines?
Sometimes certain lines, or lineages, of chickens are more susceptible to a given disease, due to their genetics. Even certain breeds seem particularly prone to some diseases.
If everything is the same between your silkies and other healthy birds, there are a few possibilities:
1) The silkies came with a vertically transmitted disease, such as Avian Lymphoid Leukosis (I am not necessarily suggesting this is what they have-- it is an example, but a possibility). This can be passed from hen to chick through the egg;
2) The silkies are genetically weak against a disease or condition that all of your chickens have, or a disease that exists in your flock, but none of your other healthy birds have shown any symptoms due to good immune systems;
3) The silkies, due to any number of factors, are experiencing chronic problems, such as severe vitamin deficiency (as an example). This can be due to deficiencies in parent stock, though usually this sort of problem will show up in chicks first;
4) A combo of the above (diseases such as ALV might not show signs except weakening the immune system).
If the silkies are being raised in any way differently than your other birds, then it would be a good idea to pay close attention to any differences.
Can you consider having another tested? Sometimes gross necropsy does not 'find' all the problems that can exist.
Were any of your birds vaccinated?
Did you get the silkies as hatching eggs, or as chicks, or as adults?
With soft bones found in the necropsy, I would be considering the possibility of vitamin D3 deficiency, click here and scroll down to "
VITAMIN D3 DEFICIENCY"
http://www.merckmanuals.com/vet/pou..._poultry/vitamin_deficiencies_in_poultry.html
Though I am still suspicious that you lost half of them during the first few days!