The predominant compliance in the dynamic response of the PUMA 560 robot manipulator arises in joints two and three. Considering compliance of these two joints, the effects of user controlled variables on system stability are studied using Floquet theory. Specifically, manipulator configuration, operating speed and trajectory amplitude are considered. For some configurations, instabilities are expected for ranges of operating frequencies which are significantly removed from the neighborhood of multiples of resonant frequencies of the stationary system. Results demonstrate overall trends in stability regions for several ranges of system configuration. Results also identify regions of rapidly changing stability of this industrial manipulator.