Steps to repro:

1. Open attached owncloud project and 't1' scene;
2. Select Terrain gameobject in the Hierarchy;
3. Go to Terrain Settings tab in Terrain Inspector;
4. Observe 'Custom material' field.

Actual result:
Terrain shader warning is thrown even though assigned 'New Material' material has Nature/Terrain/Standard shader. See attached actual.png screenshot.

Regression introduced in Unity 5.6.

Expected result:
Terrain shader warning should not be thrown for custom material having any of Nature/Terrain shaders. See attached expected.png screenshot.

Notes:
- The bug is reproducible with baked terrain lightmaps under PVR backend; not reproducible under Enlighten baking backend;
- Reproducible in 5.6.0b3;
- Not reproducible in 5.5.0p1, 5.4.3f1;
- Reproducible on both OSX 10.12.1 and Windows 10;
- Reproducible only with Nature/Terrain/Standard shader; Not reproducible with Nature/Terrain/Specular and Nature/Terrain/Diffuse shaders;