Steps to repro:

1. Open Unity;
2. Import attached 'testIncorrectYAxisInput' package;
3. Open 'test' scene';

4. Notice that there is both FPS controller (main playable prefab) and Main Camera in the scene;
5. Enter Play mode;
6. Move mouse up and down;

7. Notice that mouse y-axis transform mouse is clamped to the FPS controller (expected behavior);
8. Exit Play mode;
9. Go to PlayerSettings (Edit -> Project Settings -> Player);
10. Switch graphics API to other mode (e.g DX11 -> DX9);
11. Enter Play Mode again;
12. Move mouse up and down.

Actual result:
FPS controller's y-axis mouse transform is captured by main camera after switching graphics API, making FPS controller partly unusable. You can still transform x-axis though and move the player. See attached gif video.

Regression introduced in Unity 5.3

Expected result:
FPS controller's x and y-axis mouse transform should always be clamped to FPS controller, even after switching graphics API.

Workaround is switch off Main Camera gameobject in the Inspector.

Notes:
- Reproducible in: 5.4.0b7, 5.4.0b6, 5.3.2p4, 5.3.2f1, 5.3.1f1;
- Not reproducible in 5.2.0f3;
- Reproducible on both Windows 10 and OSX 10.11.3;
- Also reproducible at runtime (Windows standalone checked).