To reproduce:
1. Open newly attached project
2. Open scene.unity scene
3. Select NavMeshSurfaceHolder game object
4. Bake navmesh on the NavMeshSurface component
5. Enter play mode
Expected result: Agent Capsule goes to TargetCube on navmesh
Actual result: NavMesh dissapears (can be seen in Scene view, while having Navigation tab open)

Workaround: Bake the NavMesh just after entering play mode with NavMeshSurface.Bake();

Reproduced on:
Version 5.4.0a6 (f149d1e091c3)
Wed, 09 Dec 2015 11:20:16 GMT
Branch: ai/navmesh/builder