Soybeans fix nitrogen, but growing soybeans doesn't necessarily mean you won't have to put out nitrogen for the corn. You just shouldn't have to put any out for the beans. Soybeans, or any legume for that matter, don't need nitrogen fertilizer because they can obtain nitrogen for themselves. But that doesn't mean they leave lots of nitrogen in the soil. All of the nitrogen goes into the plant. When the beans are harvested, or when animals harvest the plants by eating them, then most of the nitrogen goes with the harvester. Only when the legumes are used as a green manure crop is there really an appreciable addition of nitrogen to the soil.
Something else to consider is nitrogen fixation requires a lot of energy. Legumes will use available nitrogen as they can, and then the nodules will attempt to fix the rest. For soybean seedlings and plants under stress, the ability to fixate nitrogen into usable nitrate is diminished, and the heavier the stress, the more diminished the ability to fixate. Some factors (rain and temperature) are outside of the normal scope of control. Nutrient stresses, such as other macronutrients or micronutrients, can be corrected through testing and fertilization. Correcting those deficiencies can help the plant fixate more nitrogen.