To reproduce:
1. Open attached project
2. Open Untitled scene
3. Select terrain
4. Select Paint details
5. Try to paint cubes
Expected result: Mouse position correctly corresponds with brush position
Actual result: They don't
Screencast http://screencast.com/t/Cz9ziPAm5kVt
By Design because:
In the problematic scene, the Terrain component is using TerrainData1 while the TerrainCollider component is using TerrainData (you can inspect the terrain data reference on TerrainCollider easily, but you need to switch your inspector panel to Debug or Debug-Internal to see the terrain data object on Terrain component).

Since at runtime some projects switch terrainData of the collider differently to achieve some gameplay mechanism, it is also not viable to force TerrainCollider always use the same terrainData of Terrain component.

Therefore in this case I'd recommend just assign TerrainData1 to TerrainCollider and reopen the scene. And no further warning/fixes will be done.