The LM4040 / 41 series only provide correct reference voltage when anode side is grounded. With dual polarity power supply (center grounded) if LM4040 anode goes to negative side of power supply, cathode (reference voltage) output is 1V. Simple test: with 6V battery having anode side grounded and resistor from battery anode to LM4040 cathode, LM4040 anode connected to negative side of battery, differential voltage across LM4040 is 1V.
The behavior of components is established in the SPICE Model. Which, is provided directly by the manufacturer. If you consider the behavior to be incorrect you can get in touch with the manufacturer or modify the SPICE model yourself to include the functionality you desire. When in the component browser, just select the component and click the "View Model" option.
Some manufacturers even have different models for their components on their websites.