I believe if you search Zandor's posts for "brown", "calmag", and/or "micro" you will find he mentions that flora Micro tends to stain the roots slightly brownish. It was in a thread discussing CalMag Plus and whether or not it stained the roots brown or not. If you have brown and SLIME and the roots break, it's not just stain.. it's probably root rot.

What you could do after a res change (pulling everything out, washing the res and grow tub, washing/scrubbing airstones and lines etc etc.) after you refill, put a little bit of hydrogen peroxide in the water. Wait 24 hours, THEN re-nute and adjust.

The H2O2 has the extra oxygen molecule and will kill the algae and give oxygen to the roots also until it breaks down to normal h2o after a day.