Thanks for resurrecting this thread. After many weeks of failed attempts, I have finally figured out the problems I was having, and why.
Initially I had my drip system setup in a 4x8 flood table (5" high sides) with a plastic cover over the table and 5" net pots placed in holes that were cut in the plastic covers. Anyway, like I mentioned before, after several failed attempts due to severe wilting and stress, I knew something was seriously wrong. H202 didn't do the trick, R/O water didn't do the trick, no matter what irrigation timing I used, it didn't matter, I still got severe drooping and eventually, crop failure. The big clue was that everytime I would go to empty the reservoir it would be murky/cloudy with a sky high PH, kind of smelly (like a damp basement kind of smell) and there would be a thin layer of slim covering everything. Well, needless to say that each time this happened, the cleanup was hellish. I'd run water with sodium hypochlorite (bleach) through the system (without plants of course) and clean every nook and cranny, only to start the vicious cycle again and again. Anyway, it got to the point where I almost abandoned hydroponics in favor of going back to soil.
That is until I sat down and really thought about the problem. First thing came to my mind was that it must be an environmental issue. After all, I was using high quality R/O water with the addition of H2O2, high quality 3 part nutes, in a very clean room, and checked on PH and TDS everyday. Water temperature was right on and so was the air temp, so I knew I pretty much had that part of the grow perfected, but I also knew that something was seriously wrong with the setup for it to go to shit in only a few days. That's when I thought about the root environment I had created by placing the plastic cover over the flood table. I thought it was a good idea first, as it would keep the humidity high so that when the roots forced their way out through the net pots, they wouldn't dry out, which was true, but it also created a highly humid (90%) and air stagnant root environment, which also created a great environment for pathogens to flourish.
So it was then that I decided that the cover must go. So I went out to the local hydro store and bought a bunch of two gallon nursery pots, yet another 50l bag of hydroton, then proceeded to spend the next 2 hours rinsing hydroton and filling pots. At the same time, I started 10 seedlings in 1.5" rockwool starter cubes under a T5. Anyway, fast forward to now, two weeks later, and I have 10 healthy seedlings in 2 gal pots filled with hydroton that are well on their way. I'm on a rather infrequent drip cycle right now, until such time that I see roots coming out the bottom of the pots, then I will up the irrigation cycles and the nute strength. Anyway, needless to say, when I dumped the res last night (after two weeks of use), it was perfectly clean, and had no smell. In fact the solution was still so good that I used it to irrigate my outdoor garden plants. The only negative aspect the current setup is evaporation, due to the lack of cover, but that isn't a big deal, I just add about a liter of water every day and that keeps the res full.
So it seems, at least for now, I'm pathogen free
I'll update this thread from time to time in the future as to what kind of progress (or lack thereof) I'm having.