You can't over water a hydro system... I would wonder if your roots are getting enough water, what is the normal water level of your container (if any level is kept). Hydroton doesn't hold water very well. I was going to use hydroton on my first grow but couldn't figure out how to ensure the roots where getting eough water when it was a little guy. So I went to rockwool and havn't tried hydroton again, yet.
Or you are burning the little guys, heat maybe?