The authors have redesigned a previously developed robust tracking controller for rigid-link flexible-joint (RLFJ) robot manipulators to handle flexibilities specifically induced by harmonic drive gearing. A more realistic, and consequently more complex model for the torque transmission dynamics which includes frictional losses, kinematic error and nonlinear compliance is utilised. The stability result achieved for our proposed controller ensures that the link tracking error is ’globally uniformly ultimately bounded’ (GUUB), in spite of additive bounded disturbances, parametric uncertainty, and the presence of complex nonnegligible actuator dynamics.