Step-by-step guide
If the server is a Supermicro Board with 2012 r2 installed, you can notice it won't reboot after installing updates. It will shut down the server instead.
To fix it follow these simple steps
- Go to Device Manager
- Go to view -> Show Hidden Devices
- Find Intel Management Engine Inteface under System
- Uninstall the driver
- Reboot the server (You will have to go and physically turn it back on still)
- Go to Device Manager again
- Show Hidden Devices again
- Find PCI Simple Communications Controller under Other Devices
- Disable them
- Reboot the server to test.
- If it works you are all done!


Keep in mind that Windows Update reinstalls the driver back, causing the same issue. Please monitor the updates closely.
Update July 9th 2020: Windows 2016 started showing same symptoms
If the server is a Supermicro Board with 2016 installed, you can notice it won't reboot after installing updates. It will shut down the server instead.
To fix it follow these simple steps
- Go to Device Manager
- Go to view -> Show Hidden Devices
- Find Intel Management Engine Inteface under System
- Uninstall the driver
- Turn off automatic updates for driver
- Go to system
- Click advanced system settings
- Click hardware Tab
- Click device installation settings
- Select "No (your device might not work as expected) "
- Click save changes button and exit.
- Reboot the server (You will have to go and physically turn it back on still)
- Now do another reboot to test as driver isn't loaded anymore

Archive of the link above if it ever dissapears: http://archive.is/KaAf0