I have not used them, but I know the roots are supposed to grow through the liner without a problem. It seems weird that water wouldn't penetrate them. Are you supposed to let them sit in water for a few hours before using them or something? Well your roots have got to get moisture, so until you can get some better help on this, I would be sure to poke several holes in each liner to make sure the water is going to soak the hydroton. I'd poke em especially where spray hits the liner most often.

Another thing you could do is lay your roots in some capillary matting, cut a slit in the bottom of the net pot and liner, and feed the matting through so that it gets wet. The water will seep up to the roots. Or, I don't suppose with that system you could flood the net pots occasionally? Until your roots penetrate the liner, you may just have to hand water twice daily or something. Once roots are through, no problems.

Sorry I can't help better. I'll think about it some more.