To reproduce:
1. Open attached project "NavMeshAreaBug.zip"
2. Open "TestScene" scene.
3. Find "GameObject" and "GameObject (1)" in Scene view.
GameObject->Inner NavMeshModifierVolume is not baked. And is "Not Walkable".
GameObject (1)->Inner is baked, because it's placed on a NavMesh Tile's edge.
4. Select "GameObject" in Hierarchy, and change it's Transform position to (-30, 0,53, -5).
5.Select "NavMeshSurface" in hierarchy, and in "Nav Mesh Surface (Script)" click Bake.
Now GameObject->Inner is baked.
6. Select GameObject->Inner in Hierarchy. In it's "Nav Mesh Modifier Volume (Script)" change it's Size to (1.8, 3, 1).
7.Select "NavMeshSurface" in hierarchy, and in "Nav Mesh Surface (Script)" click Bake.
GameObject->Inner is no longer baked, again it's "Not Walkable" area.

Expected result: NavMesh is baked correctly, no matter how small NavMesh is.
Actual result: If NavMeshModifierVolume area is smaller than some value, and is surrounded by a different area, it will not be baked correctly (becomes NotWalkable area).

Reproducible: 5.6.0b1. 5.6.0b3

Workaround:
Under "Nav Mesh Surface (Script)" reduce "Tile Size" to the minimum. This will increase a chance that NavMesh will be touching Tile's edge, which will result in correctly baked NavMesh, even if the area is too small. (if the area is too small and in the middle of a tile and does not touch the edge, it will still be not baked)

Notes:
Scripts use new NavMesh functionality, added only in 5.6.0b1
Changing "Min Region Area" in Window ->Navigarion -> Bake -> Advanced, will have no effect.
Might be related to 836000