one thing alot of peeps dont' do is to make sure they get the southern ag way up into the hydroton too. or whatever media they are using. root rot will hide in every nook and cranny. you could either take your nute solutiion in a gallon jug and top feed each bucket really well. or just mix up a strong batch in plain water and do the same thing. get that stuff everywhere.
if the rot is really bad, you could also hit it with sterile for a bit to kill it (peroxide, chlorine) and once it's gone for sure, then go back to southern.