NavMeshSurface does not bake certain places if they are not encompassed enough by the surface area. This only happens when the center of navmesh area is displaced.

To reproduce:
1. Open attached project
2. Open Untitled scene
3. Select Cube game object in Hierarchy
4. Bake NavMesh on the Cube's NavMeshSurface script
Expected result: The encompassed area bakes
Actual result: It doesn't

Note: If you increase the Size X variable ~60 OR Size Z variable above ~100 the area starts to bake.
Note #2: An extremely interesting result happens when you increase Size Z value to 100.
Half of the encompassed area get's baked, another half does not. Attaching a screenshot with this StrangeNavMesh.png in files.

Screencast of reproduction: http://screencast.com/t/Rh6wYYoC

Reproduced on:
Version 5.4.0a5 (806f333a7d81) Personal
Mon, 30 Nov 2015 22:54:41 GMT
Branch: ai/navmesh/builder