Steps to reproduce:

1. Open attached project "784876.zip"
2. Open scene "Scenes/testscene"
3. In hierarchy, select "BakeCube"
4. Make sure that material it uses is non-opaque (is set to Cutout, for example)
5. Open lighting window and bake lightmap

Regression introduced in 5.3.0b4 with the fix for http://issuetracker.unity3d.com/issues/error-when-baking-a-lightmap-if-object-has-a-material-with-crunched-texture-and-rendering-mode-set-to-other-than-opaque
Not reproducible: 5.2.4f1, 5.3.0b3
Reproduced with: 5.3.0b4, 5.3.4p2, 5.4.0b13