Brown algae on clone stems

I figured I would try my hand at hydroponics for the first time, and made a six site cloner. In my five gallon reservoir, I put in four teaspoons of Botanicare Aquashield. After about three or four days, the stems got soft and had some slime on the stems. I am assuming this is brown algae. I re-cut them, and put them in rockwool cubes with Olivia's rooting gel under a humidity dome.

Are my clones shot?

As long as they weren't too far gone you might see a few pop roots. Try some of the ZHO powder from botanicare, the trichoderma fungi are what you want. I had this problem and what helped me was making a microbe tea with aquashield, ZHO, and a handful of EWC, then inoculating the water. I still had to change the water every two days and re-inoculate.

Thanks for the tip.

I forgot to add that I let them sit in a bath of H202 in shot glasses

I took one gallon of pH'd water, and put in one drop of 35% H2O2 into the water, then moved some of that over to the shot glasses to let them sit for an hour.