Are the tank's tops and bottoms at the same elevation such that they are expected to fill & drain in unison?
Also check to be sure the vent lines are clear. A low spot in the hose run with some water trapped in it will prevent balancing. One test is to open the deck fills for both thanks and see if they balance. If the venting is poor, you might even encounter a noticeable pressure or vacuum when you remove the deck fill cap.