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.