I have no idea what the problem is but I once read that you shouldn't have reflective material under your plants cause the underside of the leaf is very sensitive. I'm not saying I'm right but it's just what I read.
Sounds like a sick set up you got going there. Regarding your first question about the roots being exposed to light. You don't want any light what so ever to be on thoose roots. The best way is to just spray paint the tank black