Maybe its not the rapid rooter...you know, we kinda jumped the gun with this rapid rooter thing and failed to ask you about all the other variables that could possibly cause you problems.

Have you decreased the water yet? A few posts/days ago you said that you run the water for a total of 5 hours. I'm flowering my 12"-15" plants right now and the pump is on for a total of 5 hours. If you have roots into the hydroton, you should be at about 5 minutes, every 4 hours of light for that little seedling. You're on 18/6 right?