most likely this brown coloration you are seeing is Algae. It will infact dry a green color if pulled out of the tank. Is it collecting on the power heads, rockwork, filtration intake/exhaust tubes, basically everything in the tank ? It should eventually break down. to much light will increase the growth of algae. with your ammonia and nitrites at 0 you should be looking into "real" fish to put in the tank. I was scared of this same thing but when i talked to my LFS
they said it was normal for a starting tank. As long as it isnt red in color.
at this point id say vacuum up some of the gunk on the substrate but dont mix it up to bad as it may be detrimental to your biofilter. just get the stuff off the surface and the rest should break down over time.