Sounds like a fungal or bacterial infection- is it becoming soft and yellow-brown?

Your cubes are around a pH of 6?
I would not use superthrive on new clones. Remember, superthrive is basically a Nitrogen blaster fertilizer! It makes the plants want to grow lush, green new leaves. But when you are cloning, you should WITHHOLD nitrogen because if the clone is spending all its energy making new growth, it has less to make roots.
Plus, new growth is very tender and vulnerable to disease. This is also a reason why you do not put the plants under bright light. You want them to just CHILL there and ROOT, not grow- yet.
Another thing to remember is that if you don't absolutely HAVE to mist, don't mist. What you want is to find the lowest humidity that your little plants WON"T wilt under. Misting TOO much can lead to rot.
What is the temperature under your dome?