You mentioned 4 baffles at 9" in height. when you are setting them up.
1st baffle goes flush to bottom of the tank giving you a water level of 9".
2nd baffle gets installed 1-1.5" away from 1st baffle and 1-1.5" away from bottom of tank, this is your bubble trap
3rd baffle gets installed 1-1.5" away from the 2nd and flush to bottom of tank, you are still at a 9" water level.
4th baffle gets installed at the other end of the tank flush to the bottom of the tank, still at 9" of water level.
now here is where the problem begins. when you turn on your return pump it starts to empty your return chamber. when this happens the water level will drop and create a waterfall affect from the 4th baffle.
Now if you make the 4th baffle 1.5-2" lower than the rest, when your pump goes on it will lower the water but not below the height of the 4th baffle, and won't cause that waterfall affect.
now when you install an ATO you adjust it to the running level of 9", this way you always have an extra 1.5-2" of water at all times at the 4th baffle.
If this confused you I can draw something up.