Modeling of the equilibrium in aqueous two-phase systems (A2PS) is very important for modeling the partition behavior of molecules in A2PS. Also, the study of process improvement can be made easier by the equilibrium modeling when the production and separation is combined into one stage. Flory-Huggins is a simple model and can be used for equilibrium calculations. This paper focuses on the numerical problems associated with the thermodynamic equilibrium formulation and attempts to show the effect that the proper scaling and optimization objective function has on the accuracy of the solution.