IMHO I would try using some chlorine or some Zone at heavy strength. I find that having a sterile res in hydro works best for me but YMMV. I think you should also take your hydroton and wash it in hot water overnight then let it dry, then put it in the oven for an hour or so at 350. I have found this to work wonders at killing bacteria and fungus that can remain in the pores. Otherwise it's best to always use new washed hydroton for every grow. I am not sure if this will do the trick for you but you may also consider that since you changed to hydroton you might try upping the amount of times your watering and make sure your not watering anymore 1 hour prior to lights out. Just some food for thought, good luck and happy growing.
KnB