LIGHT! Trust me on this one man. It looks like you are using a grey tub for DWC right? I was doing the exact thing and my roots were doing it too. I finally bought another tub and spray painted it flat black and started using it. I was not only getting brown spots, but also slime on my roots. Nasty stuff...since I changed tubs though, I have not gotten any browning, slime and my roots are healthier than ever. I'll post a picture tomorrow, seriously the only brown on my roots is from the previous damage. Also, lower the water to 1-1.5" if you haven't already.