Is this a flood and drain system, or NFT system? I'm not sure if anything is really wrong, some root discoloration (yellow, or light brown) is not necessarily bad. But is usually either on older roots, or roots stained by the color of the
nutrients. Although from the pictures it looks like the plants in the cups hang down farther. That is ,that the bottom of the rockwool cubes is higher than the bottom of the cups. Therefore it's not nearly as noticeable on the plants in the cups, simply because their roots are closer to the water level.
P.S. Just curious, is that vinyl fence post tubing? I'm needing some 4 inch square tubing, but vinyl fence post tubing is too expensive for what I need to do.