Gnats can cause root damage which will look like root rot. Maybe that's what's happening. Especially since you believe your soil/nutes are dialed in?
I control gnats by laying a piece of posterboard over the top of the container. I cut a round piece, and a slot to the center. I make two and lay them over the container in a way to cover each other's slots. Then all I have to deal with is the drain holes. I spray some pyrethium or an organic rosemary/peppermint/clove mixture around the drain holes. It irritates the gnats and they stay away. (Some people put their containers in panty hose to cover the drain holes.).
I bet that's it. (EDIT: Unless you're using a new bag of soil. Maybe you got a bad bag and it really does have a moly problem. Moly def seems unusual/rare if you're not overwatering.).