Reproduction steps:
1. Download unitypackage attached. (StutteringTestProject_1.unitypackage)
2. Create new project.
3. Import unitypackage.
4. Open scene "Stutterring_Test_1". (Assets -> MFK -> "Stutterring_Test_1")
5. Press play.

Expected result: FPS stays stable.
Actual result: sometimes FPS drops unexpectedly.

Note:
Use profiler to get more information. Sometimes Gfx.WaitForPresent appears.
If you delete scripts and turn off VSync, it only works if you restart Unity. (another issue).

Reproduced on 5.3.7p2, 5.4.3p3, 5.5.0f3, 5.5.0p1, 5.6.0b1.