We investigate the instability and dynamical properties of nanoelectromechanical systems represented by a single-electron device containing movable quantum dots attached to a vibrating cantilever via asymmetric tunnel contacts. The Kondo resonance in electron tunneling between the source and shuttle facilitates self-sustained oscillations originating from the strong coupling of mechanical and electronic/spin degrees of freedom. We analyze a stability diagram for the two-channel Kondo shuttling regime due to limitations given by the electromotive force acting on a moving shuttle, and find that the saturation oscillation amplitude is associated with the retardation effect of the Kondo cloud. The results shed light on possible ways to experimentally realize the Kondo-cloud dynamical probe by using high mechanical dissipation tunability as well as supersensitive detection of mechanical displacement.