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The paper documents fatigue related mechanical failures in variable frequency drive (VFD) motor machinery due to mechanical vibrations excited by drive torque harmonics which are created by PWM switching. Present effort models the coupled system with full electrical system including rectifier, DC bus, inverter, motor, and an industrial mechanical system including flexible couplings, gearboxes and multiple inertias. The models are formed by a novel combining of a commercial motor code with a general, self-written mechanical code. The approach extends failure prediction beyond simple occurrence of resonance, to fatigue life evaluation based on Rain-flow algorithm, which is suitable for both steady state and transient startup mechanical response. The second contribution is a demonstration that the common use of multilevel inverter to reduce voltage/current harmonics may actually exacerbate resonance and fatigue failure. This is shown to be caused by a resulting amplitude increase of torque components in proximity to potential resonance frequencies.