Steps to repro:

1. Open attached project and 't1' scene;
2. Select Terrain gameobject in the Hierarchy;
3. In Terrain Inspector go to 'Paint Texture' tab;
4. In the pallette select second white texture;
5. Try to paint white texture on terrain with using one of terrain brushes.

Expected result:
Texture is painted on terrain.

Actual result:
- Texture is not painted;
- Error:

Exception: Float array size wrong (layers should be 2)
UnityEngine.TerrainData.SetAlphamaps (Int32 x, Int32 y, System.Single[,,] map) (at C:/buildslave/unity/build/artifacts/generated/common/modules/Terrain/TerrainDataBindings.gen.cs:656)
UnityEditor.SplatPainter.Paint (Single xCenterNormalized, Single yCenterNormalized, Int32 splatIndex) (at C:/buildslave/unity/build/Editor/Mono/TerrainEditor/TerrainInspector.cs:121)
UnityEditor.TerrainInspector.OnSceneGUICallback (UnityEditor.SceneView sceneView) (at C:/buildslave/unity/build/Editor/Mono/TerrainEditor/TerrainInspector.cs:1892)
UnityEditor.SceneView.CallOnSceneGUI () (at C:/buildslave/unity/build/Editor/Mono/SceneView/SceneView.cs:2397)
UnityEditor.SceneView.HandleSelectionAndOnSceneGUI () (at C:/buildslave/unity/build/Editor/Mono/SceneView/SceneView.cs:1715)
UnityEditor.SceneView.OnGUI () (at C:/buildslave/unity/build/Editor/Mono/SceneView/SceneView.cs:1585)
System.Reflection.MonoMethod.Invoke (System.Object obj, BindingFlags invokeAttr, System.Reflection.Binder binder, System.Object[] parameters, System.Globalization.CultureInfo culture) (at /Users/builduser/buildslave/mono/build/mcs/class/corlib/System.Reflection/MonoMethod.cs:222)

is thrown. See attached video.

Regression introduced in Unity 2017.1.0a6.

Notes:
- Reproducible in 2017.1.0b1, 2017.1.0a6;
- Not reproducible in 2017.1.0a5, 2017.1.0a4, 5.6.0f3, 5.5.2p1;
- Reproducible on Windows 10 and OSX 10.12.3;
- The bug doesn't affect painting of grass and detail meshes.