How to reproduce:
1. Open attached project "CommandLineArguments.zip" and scene "SampleScene"
2. In Unity Editor menu, select File -> Build Settings -> Build -> select "Build" folder located in the projects directory (if asks, application name must be "CommandLineArguments")
3. After building the project, go to the "Build" folder and open "StartMedium.bat"
4. In top-left corner observe "QualitySettings.GetQualityLevel(): ..."

Expected result: QualitySettings.GetQualityLevel(): Medium
Actual result: QualitySettings.GetQualityLevel() is not Medium (saves the last quality setting, it will be either Potato or Ultra)

Reproducible with: 2017.4.16f1, 2018.3.0f1, 2019.1.0a10

Not Reproducible on Linux with 2019.3.0a7, 2019.1.0f2