I am sorry that my english is not good.This last post might be a Microsoft and/or bios issue, that I too am experiencing on W10. Ever since the rise of UEFI this issue seems to be more prevalent. I've spent the last many days trying to resolve this same frustration. Windows keeps trying to boot to my USB sticks or my backup SSD drive, even though my bios has the boot order set properly, I tried changing around the sata cables, reformatting every drive, resetting the bios, clearing cmos, etc. Nothing is really solving it, and Google has a ton of people experiencing the same problems with no universal solution (people that aren't even using NTLite). The worst part is some of the issues are intermittent which makes it harder to troubleshoot.
However, I will say that the issues became more prominent after I moved to the latest NTLite version from June 11. Could be coincidence, but also maybe not. I just recently got the "Windows could not update the computer's boot configuration." after Windows Setup was finished, which is something I never saw before, and my NTLite stuff shouldn't be the cause of it. Now all of a sudden I have to physically remove my USB drive from the device or hit F10 and manually boot to my primary SSD after Windows Setup is done.
I didn't quite understand what you meant.
I understand you seem to mean the boot is missing or corrupted.
If the error you said was about MDT, I've solved it by writing an extra script.
The following is my MDT solution (Chinese).
环境Windows Server 2012 Standard x64DC林功能级别：Windows Server 2008 R2域功能级别：Windows Server 2008 R2Windo...
Microsoft Deployment Toolkit Scripts. Contribute to Shankschn/MDT-Scripts development by creating an account on GitHub.
However, this time I want to implement an unattended installation system that is not based on internet.