I am honestly leading towards the weir being clogged. If I have the ATO on the level in the 3rd chamber stays low and it just pumps the water and overflows the display. I will have the tank completely filled and it will manage to do this within hours.Agree with above. It doesn't make sense that you are experiencing an issue with all media and sponges removed from the system. Make sure that when the return pump is running, you have enough water in the third chamber prior to turning on the ATO. Once you have the right water level then turn the ATO on and it should maintain the level where your sensor is. That's all there is to it. If that still doesn't correct any issues then I have no clue what else it could be other than the weir getting clogged. But that should be very noticeable and if bad enough would make the tank overflow.
I will send some pictures of water levels with the pump on, and off once I get home.