The presence of slowly varying signal drifts or low frequency (subharmonic) contributions can produce significant errors in the calculation of phase shifts using a correlation analysis. Under these conditions, the phase shift calculation becomes dependent on the reference signal phase angle. In this paper, we propose a modification to the correlation analysis to remove this dependency. We also present our analysis in discrete form to enable a digital implementation. Finally, we discuss the adverse effects that changes in the limits of integration can have on the phase shift calculation under the presence of linear signal drifts.