post a pic so i can help you out a little
i use botanicare as well. i asked around about the brown roots in fear of rot and its just a side effect of the liquid karma. so yea if your using an organic nute solution i would say your fine. but if not look for things that may be contributing to a bad situation. is your resevoir light tight? is it a solid dark color? and how often are you changing out nutes? how about the water temp? these are the main things i have checked countless times to make sure. also when you change your nutes i bathe my roots in ph'd water, so you could try that. just some friendly ideas that might help.