How to reproduce:
1. Create a new project
2. Download Cache server http://unity3d.com/unity/collaboration/
3. Go to Edit> preferences> cache server and change IP address to localhost
4. Go to Editor project settings and make Version control "Visible meta files", Asset serialization "Force text"
4. Create some prefabs and materials
5. Give them an AssetBundle names
6. Close the project and delete its library folder
7. Reopen the project, check the object
8. You will notice that some of it doesn't have AssetBundles

Note:
-Notice that if you right click on "Assets" and choose "Reimport All" that these
asset bundle name assignments are still not imported properly.
- If you select each asset individually and right click and choose "Reimport", then
the bundle name is imported properly.