Sirry I could not find this post or a reply yo a post. Maybe someone could find this post(It was for black stain or algae).Any rate, I had read a book a couple of months ago (Marine Reef Aquarium Handbook). The black or grayish look to your substrate is Noxious Sulfide producing Anaerobic Iron Bacteria according to Dr. Robert Goldstein (1997). What is the grain size that you were using for your sand base? Sorry for the delay and thank you if this post can be found.
Later,
The Chef
Later,
The Chef