Steps to reproduce:
1. Open the attached project (New Unity Project 3.zip) or create a brand new project
2. Go to Build Settings, switch platform to WebGL
3. Go to Build Settings and click Build/Build and Run
4. Error messages appear in Console Window:
Failed running D:\Program Files\Unity\5.6.0b3\Editor\Data\il2cpp/build/il2cpp.exe --convert-to-cpp --development-mode --compile-cpp --libil2cpp-static --platform="WebGL" --architecture="EmscriptenJavaScript" --configuration="Debug".......
Exception: D:\Program Files\Unity\5.6.0b3\Editor\Data\il2cpp/build/il2cpp.exe did not run properly!
Exception: D:\Program Files\Unity\5.6.0b3\Editor\Data\il2cpp/build/il2cpp.exe did not run properly!

Reproduced with: 5.6.0b3
Not reproduced with: 5.3.6p8, 5.4.3p3, 5.5.0f3, 5.6.0b2
Regression introduced in 5.6.0b3