3.3V regulator does nothing for first ~12 seconds after power-on, then outputs 5 volts
Short answer : The TPS78633 NR pin is incorrectly connected to 3.3V output, and it is causing the issue.
This overrides the internal Vref of 1.25V with the output voltage, and it tries to set the output voltage high enough so the divided feedback matches the reference voltage, so basically, the regulator just fully passes input voltage to output.