Steps to repro:

1. Open Unity;
2. Open attached project and '350-LODFading-subset' scene;
3. Select 'Percentage LOD Object' gameobject in the Hierarchy;
4. Observe the bounding box;

5. Bounding box is not aligned with the LOD group actual object (see attached actual.png screenshot);
6. Press Recalculate Bounds button in the LOD Group inspector;

7. Observe that now LOD bounds are aligned with LODGroup - EXPECTED (see attached expected.png);
8. Save scene;
9. Switch to other scene of the project;
10. Switch back to ''350-LODFading-subset' scene;
11. Repeat step 3-4;

12. Observe that LOD Group boundaries are still misaligned with LOD objects.

Expected result:
LOD bounds should always preserve the same value after saving and switching scenes.

Notes:
- Reproducible in 5.5.0a1 graphics/instancing/lodfade, 5.5.0a1, 5.4.0b23, 5.3.5p1;
- Reproducible on both OSX 10.11.4 and Windows 10;
- Also reproducible when saving scene and reopening Editor.