Unsteadiness of a shock dominated hypersonic flow including shock wave boundary layer interactions and flow separation over a double cone, double- wedge and’tick’ configurations are investigated. The time accurate DSMC solutions combined with global linear stability and the residuals algorithm provide an opportunity to determine the damping rate, frequency and amplitude function of the least damped eigenmode. The residuals algorithm also permits predicting the corresponding steady state solution at a fraction of the DSMC simulation cost. It is observed that the time required to reach steady state is conditioned by the separation region and the shock wave boundary layer interaction. The oscillatory behavior of the residuals close to convergence in the double wedge calculation for the reacting air case can be explained by the existence and slow temporal decay of traveling linear global modes.