I tried out the save, that's really odd.
It's all walled and floored off and covered, I checked all the tiles, and they're all constructed. The bottom area is full, and water appears on the top area, but it continues to fall down into the bottom area and disappear. If I stop the pump, the bottom layer remains full, and if I breach the bottom layer, it all drains out until it's dry, so it's not acting like an aquifer. If I then turn the pump on, it will refill the bottom layer like normal, but when it gets full, the water still keeps pouring down into it and disappearing. If I floor off the second level, it'll fill up to full like normal, but if I make a hole in the floor, it'll all drain down, even though the area beneath it is full of water. And I tried draining it into a new tank that I constructed with the same results. It'll still pour down and fill areas beneath it, but it doesn't stop pouring down when the levels below it are full.
It's like it's not recognizing that the level below is full of water, and the water is still falling down anyway, and just disappearing if the level below is full. It's also not transmitting any pressure like it normally would if it were resting on top of water on the level below, this doesn't happen with transitions between other levels as far as I can tell.