I'm not too familiar with the ADA system, but I seem to recall some other components that are sometimes used as layers. Maybe if you're using those, and the gravel vac will upset them, then you might wait and see if it eventually mends itself.
Otherwise, I vote for the vac. Something is obviously still affecting your new plants. Unless you've missed something important or aren't telling me about it, a fouled, anaerobic substrate is the only possibility I can think of. Anaerobic substrates can produce hydrogen sulfide gas, which is quite poisonous. This would certainly do a number on your plants, maybe even prevent normal bacteria from moving back in.
i could not smell anything from the substrate but my arm smell like Cyno, even though there is no cyno in the tank.
it says rooted plants suppose to grow in it am confuse
Rooted aquatic plants are well adapted to growing in an anaerobic substrate. They are able to ‘pump’ enough oxygen to the roots so that in many cases the oxygen actually diffuses into the surrounding sediment. They can also respire anaerobically if necessary and produce lactic acid or ethanol instead of CO2 as a byproduct. The root meristems (growing tips) of some species are even inhibited in the presence of oxygen.