The issue seems to caused by having a second camera with specific settings in the scene

To reproduce:

1. Open the project, attached by the user (UnityProject.zip)
2. Open the "Default" scene
3. Build and run for WebGL
4. When the game is run, press Change Rect button

Expected: changing pixel rect of the camera at runtime doesn't stop it from rendering the scene
Actual: the cube stops spinning in the scene when camera's pixel rect is changed at runtime

Reproduced in 5.6.0a1, 5.6.2f1, 2017.1.0f2, 2017.2.0b2
Did not reproduce in 5.5.4f1
Regression introduced in 5.6.0a1

Fixed in 2017.1.0p3