I had this exact same problem. The issue is that my tank is in an alcove with less than 12” clearance on each side, so I could not see the level indicators on the sides. I would look in the tank and the level looked great. My ATO was working fine. I would look in the skimmer compartment (behind the gate) and the level was fine. However, one day I had the hood totally opened and just happened to notice that the water level in the right side pump compartment was a good 6” lower than the tanks water level. Turns out I had the sponge crammed in too tightly and it was restricting the water flow to the point that the chamber was being pumped out faster than it could be replenished. I didn’t cut the sponge – I just adjusted it so it was not packed as tightly. That totally fixed my issue.
Happy reefing!
Morgan