I've been watching brown on my roots for a week now, since I started giving them nutes(AN connoisseur with b-52) similar to yours, heavier/darker at the water line fading out down, above the water line is nice and white..I'm thinking it's my nutes staining them possibly some residue from not rinsing the rocks out well enough. I just did my first nute change and there was a reddish/brown residue when i cleaned the bucket out..leading me to think it was the rocks or an additive. Everything was squeaky clean, no sliminess or anything when i changed it out and smells good..I'm more of the wait and see type, too many times people overreact to these situations and make things worse.