Your choice of nutes are notoriously inconsistant between batches.
I used them 3 times---2 were fine, 1 killed my plants.
I now use Advanced nutrients sensi grow/sensi bloom 2 part mixes.
General Hydroponics brand is iffy at best.
Did you mix it correctly before adding to the bucket?
Some cheat and mix the whole 4 gallon batch in the first gallon and top off with water----bad idea.
As for water level, I top the bugger to the very top at transplant, and then let it fall to the bottom of the basket naturally, I let about 2 gallons get used up before filling again to the bottom of the basket.
Transplanting in pebbles, I make sure the rootball is well seperated and cleaned, and placed at the very bottom of the basket. Someimes it means the stem is covered to the first leaves, but it doesn't seem to hurt them.
Even so, I have 4 root spa's just like yours, with 3 plants in each one------and 1 single plant turned out like your damaged example. Brown roots, no growth, died.
I figured that I damaged the stem during transplant, or didn't get the roots clean enough before hand.