Its there because when the water falls over from the 2nd and 4th chambers into the 1st and 5th chambers its rather like a waterfall and so drags bubbles down right into the pump area on te side chambers. The bubbles then get sucked into the pump and blown into the display. You need to keep the water level high enough so that the waterfall is as small as possible...ie make sure the water levels between chambers 2nd+4th compared to 1st+5th are almost the same...that way you wont get the waterfall effect causing bubbles in 1st+5th chambers.
Also, JBJ supplied the tanks with two extra sponges that go on the 1st+5th chambers to catch the bubbles. Make sure you are using the sponges if the water levels arent similar as they will tap air bubbles preventing them from being dragged into the pumps.
AS I keep my water level almost the same by toppng up daily, I dont need to use the sponges. Also, if the tank is new for some reason the effect is more. My tank gets NO bubbles in the display area.
HTH.