To reproduce:

1. Download attached project "queriesHitBackfaces.zip" and open in Unity
2. Open "test" scene
3. Press "Play" button
4. Open "Scene" view
5. Move "Sphere" game object inside of "Cube" game object on "Scene" view

Expected result: After you you move "Sphere" game object inside of "Cube" game object, Raycast or Sweep detect the backfaces of the "Cube" game object
Actual result: After you you move "Sphere" game object inside of "Cube" game object, observe that neither Raycast or Sweep detect the backfaces of the "Cube" game object

Reproduced on Unity 5.5.3f1, 5.6.0f3 and 2017.1.0b1

Could not check for regression in 5.4.x, because files can not be loaded