Any ammonia readings in a tank containing critters is terrible. Did you get ammo readings prior to the substrate change in these tanks?In the two 10 gallons, I've had deaths and ammonia readings that weren't terrible but weren't great.
I've been really good at regular water changes lately (last couple of months after my broken foot healed) and did even more tank cleaning with the ammonia readings but it seems to get toxic really fast. I also have lots of live plants.
Like tanker suggested, it sounds like the majority of the beneficial bacteria in this tank was in the old substrate. Maybe the filter cannot house enough for the bio load in this particular tank.
I guess big water changes and heavy doses of Prime for the meantime.