Some shafting systems, such as those in certain types of rotorcraft, are mounted on flexible foundations. Since the foundation can deform, shaft segments are joined by flexible couplings to accommodate motion. Many of these couplings are non-constant velocity, meaning there is a difference in angular velocity between the input and output of the coupling, and this difference can lead to large motion in the shaft system. In this paper, a model is developed which allows the misalignment angle between the input and output shafts to vary dynamically with time, and this kinematic relationship creates a nonlinearity in the system. Through nonlinear analysis and accompanying simulation, this research explores some interesting and potentially harmful phenomena which occur at secondary resonances of such a shaft system. At particular shaft operating speeds, the shaft system may experience internal resonance, large and rapid amplitude growth, or chaotic motion, all of which can lead to destructive large amplitude vibration. This paper also shows that applying appropriate damping is an effective strategy for mitigating these effects.