A study of the crank and gear-train dynamics of a two-stroke opposed piston diesel engine design uncovered a disconnect between the thermodynamic process and its conversion to mechanical work. The classic two-stroke opposed piston design phases the intake piston to lag the exhaust piston in order to achieve favorable gas exchange, overcoming the disadvantage of piston-controlled ports. One result of this is that significantly more of the engine torque is delivered by the leading crank than from the trailing one. This paper will examine why this torque difference occurs showing that it is not simply a proportioning of the available thermodynamic work but a result of a fundamental mechanical loss mechanism that limits the achievable brake efficiency of this engine architecture. This analysis will provide a basis for developing effective design solutions to overcome the mechanical loss by providing an understanding of this loss mechanism.