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Phase flicker has become an important performance parameter for the liquid crystal on silicon (LCOS) devices. Since the phase response of the LCOS device cannot be measured directly, it is usually derived from the intensity response of the modulated light beam when the LCOS device was placed between a pair of crossed polarisers. However, the relationship between the intensity of the beam and the phase response of the LCOS device is periodic. This would lead to uncertainty in the phase flicker measurement. This paper analyses this measurement uncertainty through both simulation and experiments. It also proposed a strategy to minimise the uncertainty.