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Due to the significantly reduced cost and effort for system calibration time-division multiplexing (TDM) is a commonly used technique to switch between the transmit and receive antennas in multiple-input multiple-output (MIMO) radio channel sounding. Nonetheless, Baum et al. (2004) have shown that phase noise of the transmitter and receiver local oscillators, when it is assumed to be a white Gaussian random process, can cause up to around 100 % errors of the estimated channel capacity of a low-rank MIMO channel when using the standard channel matrix estimator. Experimental evidence shows that consecutive phase noise samples affecting measurement samples collected with real TDM-MIMO channel sounders are correlated. In addition the spatio-temporal aperture induced by the selected switching schemes has an impact on the ordering of the phase noise samples in the estimation of the channel matrix estimate. This paper investigates how both effects affect the channel capacity estimator based on the standard channel matrix estimator. We show by means of Monte Carlo simulations that by using an experimentally obtained ARMA model of phase noise the predicted error of the ergodic capacity estimate is reduced compared to the case where phase noise is white and Gaussian. We also show that the estimated ergodic capacity is highly influenced by the choice of the spatio-temporal aperture.