To reproduce:
1) Download attached project
2) Download PsTools (notably, PsExec) - https://docs.microsoft.com/en-us/sysinternals/downloads/psexec
3) Run cmd in administrators mode
4) Run the PsExec like this - "psexec -i -s cmd.exe"
5) Run your Unity in batchmode like this (you can use 'cd' to move to the folder and add logging message if you want it to be more conveniently placed):
<pathtounity>\Unity\Editor\Unity.exe -batchmode -buildWindowsPlayer tmp\test.exe -projectPath <path-to-repro-project> -quit

Expected: It builds normally (it does so when built from editor ran explicitly)
Actual: Compiler errors are found

Reproduced in 2017.2.0f3, 2017.3.0b6, 2018.1.0a1