Steps to reproduce:
1. Download attached project
2. Delete all project files besides Assets and Project Settings
3. Build it For standalone through console with the following example arguments
"D:\Program Files\Unity 5.6.0b1\Editor\Unity.exe" -projectPath "D:\Downloads\case_925913-MissingTexturesAfterBuild" -batchmode -nographics -buildWindows64Player ./Missing.exe -quit
4. Run the build

Expected result: texture is displayed on screen
Actual result: texture is not displayed until manually reimported or -nographics argument is reported

Reproduced on 5.6.0b1, 5.6.2p1, 2017.1.0f2, 2017.1.0b1
Not reproduced on 5.5.4f1, 5.6.0a5
Regression introduced in 5.6.0b1

Verified FIXED 2017.2.0b6 and 2017.3.0a3