To reproduce:
1) Open the attached project and load 'PPU - 1to1' scene
2) Select 'Parent' game object in hierarchy and play the scene
3) Zoom in and check colliders of child objects in scene view. Notice that 'player' game object rests on the corners of other two cubes (it bounces off in 4.6 and falls into the gap, probably that is expected)
this behavior is expected.
4) Now load 'PPU - 100to1' scene and repeat step 3. Notice that 'player' game object does not fall fully to the corners of another cubes (in 4.6 it does not bounce off into gap...might be a bug, that scale changes physics simulation). This is not expected.

You can check screenshots made by user for more info.