Could you post a pic?
When my tank was setup for 3 mos, I started to see dark brown diatoms covering the plants, glass, and rocks. I am assuming that it also covered my substrate, but I really couldn't tell because of the dark brown color. After a few weeks, it just went away. Now, I have a couple of big pieces of sandstone that are covered with bright green fuzzy algae on one side and black fuzzy algae on the other side. Perfectly normal, I was told. When it gets to me, I yank out the offending rock and scrub it clean. Of course, that's really not an option with substrate.
I have the tank lights on a timer for about 9 hours a day.