Todd, in the moment its hard to imagine what happens. For both VDD and VCC the Duty cycle is at or above the Limit Duty max. That's wrong. Its weird both SMPS are with the same problem. I would test both sub PCB off line (see
QMX QMX_Plus Power supply test Process).
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If the SMPS boards are ok you may go a second step. To have consistent data produce a screen shot from diagnostics and check in the same state all voltages at the two pin header of the SMPS. If an oscilloscope is available check PWM_3V3 and PWM_5V for duty cycle and voltage min / max and also ADC_3V3, ADC_5V, VCC and VDD for ripple.
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73 Ludwig
