Formal constitutional systems of separated powers often fail to sustain meaningful systems of checks and balances in presidential-style democracies. What conditions support balance in the separation of powers and what conditions provoke instability and conflict? We draw on Madisonian political theory and research addressing the separation of powers in the United States to develop a game theoretical model of inter-institutional stability and conflict within a separation of powers system. Two factors emerge as catalysts for institutional instability and conflict among the branches of government: high-stakes institutional rivalry combined with uncertainty about the publics relative support for various branches of government. We apply the model to the experience of Honduras in 20082009 that resulted in the coup ousting President Zelaya which illustrates the difficulty of developing credible checks and balances.