Changes made to the VR Support toggle in Player settings appear to not persist the next time you open the project and look at the toggle in the UI. But when you enter Play mode whether or not the scene actually appears in your VR headset does depend on how you set the VR Support toggle during your previous Editor session.

So, there are situations where VR Support behaviour does not match the VR Support toggle state in the Player settings UI.

This is a regression compared to Unity 5.4.0p1.