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This paper analyses the natural voltage-balancing characteristic of a three-phase flying capacitor multilevel converter when it is operated under the spectrally optimal Phase Disposition (PD) pulsewidth modulation (PWM) strategy. Using this analysis, it is shown that PD PWM has superior balancing characteristics compared to the phase-shifted carrier PWM strategy, because it places more spectral energy into the differential-mode sideband harmonics that drive the voltage-balancing process. From this understanding, an alternative balance booster filter network connection is proposed that significantly improves the natural balancing response of a flying capacitor converter for either PWM strategy. The analysis is confirmed by extensive simulation and experimental studies.