To reproduce:

1. Download attached project "Platform test.zip" and open in Unity
2. Open "test" scene
3. Enter to Play mode
4. Press "E" button on your keyboard and hold it

Expected result: In Game window you will see that "player" game object will always flash red
Actual result: In Game window you will see that "player" game object will flicker with red and white colors once per frame

Note: Holding "E" button will let a class run a method to modify the Collider Mask, regardless of what you set it to, the Collider will turn off completely for a frame.
Note: In the Inspector for the "Platform" game object, changing the Rate of the Platforms script will change how often it updates - no matter the rate the next frame will always skip the collision. The "player" game object will flash red when its collider is not touching the platform and white when it is.

Reproduced on Unity 5.5.3p4, 5.6.1p2, 2017.1.0b8 and 2017.2.0a1