System76 support here. One of the important final steps to the firmware update is that 'load setup defaults' needs to be issued manually in the BIOS. The hard

System76 support here. One of the important final steps to the firmware update is that 'load setup defaults' needs to be issued manually in the BIOS. The hardware has a limitation that even after we apply the new firmware, the settings have to applied by a manual step. This is written out in the firmware flashing steps, but it's still easy to miss! Please 'load setup defaults' in the exit tab of the BIOS (F2 on boot), at which time the Intel Management Engine will be fully disabled, and future firmware prompts will cease. If you are still getting the prompt, please reach out at support.system76.com and we will help further!