http://screencast.com/t/QguCezuU
To reproduce:
1. Open attached project
2. Open NavMeshIssue scene
3. Enter play mode
4. Drag around the capsule to control the cube's destination
5. Observe that it cannot pass through some spaces
Expected result: It can pass through all the places
Actual result: It goes around them
Note: if you take the 4 Movable Puzzle Piece game objects and remove the Obstacle component from them, set them as static and bake the NavMesh the areas become passable.