I set up a small El-natural tank once with an inch of plain topsoil and pea-gravel, this was the only El-natural tank that utterly failed

. The larger sized substrate cap quickly made the substrate go anaerobic and all of my plant's roots turned black. Now I only use coarse sand for the cap, and if I use decorative stones they are placed against the bottom glass first and then the soil is placed around the stones...this keeps the stones from compacting the soil and creating a very bad mess!
You might want to pull up one of your plants and check the roots, also check for any foul smelling bubbles that surface
