The phase stability of mixed-cation alkaline-earth hexaborides is studied. These materials have the potential for use as hydrogen storage sources. The results show separation of the MB6 phase into multiple solid solutions with varying compositions in ternary (Ba-Ca)B6 and (Ba-Sr)B6 powders. X-ray diffraction data contains peak splitting and asymmetry and high-resolution transmission electron microscopy confirms the presence of these phases in the form of homogenous nano-regimes in individual equilibrium. Thermal treatments ranging from 1000-1700°C enhance the overall homogeneity of the samples and merge the phases into one, indicating that the as-synthesized state is thermodynamically unstable as the collection of nano-regimes results in increased microstrain and lattice imperfections. Analysis of the chemical reactions that occur during synthesis suggests that the decomposition of the metal precursors (nitrates and carbonates) to metal oxides introduces variance into the formation process of mixed-cation hexaboride compounds, producing nano-regimes within the crystal lattice.