Oscilloscope image 1, yellow is 3V3 (SYS_VIN_SV), after 60ms, green 12V (SYS_VIN_HV) and blue 5V (SYS_VIN-MV) are powered on
This looks ok.
Image 2, yellow 5V (SYS_VIN_MV), followed by a delay of more than 50ms through RC for the green MODULE_POWER_ON. Then the module starts to power on, and after the power on is completed, the blue CARRIER_POWER_ON is pulled up. At this point, the carrier board starts to power on, and after about 800ms, the module actively lowers the CARRIER_POWER_ON.
The RC for MODULE_POWER_ON looks ok also. The circuit it drives has VIH of ~2V and ultimately results in the CARRIER_POWER_ON signal going high, which you do see on your capture. As mentioned in the Design Guide, CARRIER_POWER_ON pulls up to 3.3V on the module, and that rail is controlled by the power sequencer. CARRIER_POWER_ON going low means the power sequencer deliberately turned the 3.3V rail off for some reason.
Afterwards, lowering the SYS_RESET_N of the module cannot cause the module to reload Flash. Only by shutting down the power and restarting or lowering the MODULE_POWER_ON can the above process be repeated.
This makes sense - the SYS_RESET_N does not affect the power sequencer. The power sequencer can only be recovered by the MODULE_POWER_ON or a power cycle.
The input signals to the power sequencer that can cause shut down are overtemp detected by a thermal sensor monitoring Thor and its own local temp, the carrier asserting VDDIN_PWR_BAD_N low, or the Thor SoC itself triggering the shutdown.
Can you confirm that the carrier board does not assert VDDIN_PWR_BAD_N low?
Are you able to check if the MODULE_SHDN_N signal goes low? This would indicate that an input signal to the power sequencer caused it to shut down. Otherwise, the power sequencer itself has its own thermal shutdown as well.
What is the cooling setup when this happens? Would you be able to provide a photo of the module and its cooling solution?
Our power supply on the carrier board was not connected to the module for testing. We saw that there is a PMIC control on the carrier board in MB1. I wonder if this is the cause of our problem?
Can you please explain this further or perhaps provide a diagram to show what you mean?