First, make sure that there is no bleach residue in the container. If you think you've rinsed it out enough, do it one more time. If you have neoprene collars make sure you either replace them or clean them very very well. There could be a few reasons why you are getting root rot.
First, make sure your water temperature isn't too high. With summer time the water temps can get pretty high. Keep it around 70-75 and you should be good. Bacteria growth take off in high temps.
Second, your pH level needs to be between 5.5-5.8 for aeroponics. This isn't soil or hydro a pH of 6 is getting too high. If you don't have a digital pH meter you might want to get one. We have a Hannah digital waterproof combo meter for about $150. Believe me, it's waterproof! It also has a temperature reading.
Third, you don't need sm 90 or anything like that. Some people do use some clone solution in their water but you don't necessarily have to. You can add 3% hydrogen peroxide (H2O2 to your water to help prevent nastiness. Add about 1 tablespoon (the measuring kind, not the one you eat with) of H2O2 per gallon of water.
Make sure you pH test after adding anything into the water.