sounds like root-rot ... try a good flush with hydrogen peroxide and clear water ... try a half-pint H2O2 per gallon, let it cycle overnite, if doesn't look better, kick it up to a pint, per gallon, and repeat ... I never used the ebb & flow style, but that sounds like a lot of pumping time ... don't let the roots dry out, but I don't 'think' they need to be kept that wet ... just my guess ... good luck :smokin: