Something must've happened. I have done what you did numerous times, move the gravel, water and filter in to a brand new tank and never suffered a loss..
It sounded like you did everything right, I'd try to investigate what caused them. Is the tank still running ?
How long was the 120 up and running before you took it down ?
If the 40 G was running, then it should be okay. It's odd that you loss fish in 2 tanks at the same time.
Was there power outage ? how long were the fish in the 40 and 30 gallon breeder ?
stan