The brown stuff is called biota, i get it all the time and its actually a good thing to have in your system,( bad for your emitters though) what biota is.... is a bunch of living organisims that are living and growing in your system that are actually all the health benifical orginisims that are suppose to be in a
hydroponic system. Take a sample and look at it under a microscope it will be teaming with microbes and nematodes. here is a link to explain>>>>>>>>>>
http://www.youtube.com/watch?v=y-wpbhnom70
I almost forgot..... what nutes are you using ?