Steps to reproduce:

1. Open attached project
2. Open scene "BuildAssetBundleFromHere"
3. Notice that mesh isn't deformed
4. Open Asset Bundles top menu and check Build for PC. In same menu click "Build Asset Bundles"
5. When building is done, drop created asset bundle to "StreamingAssets" folder
6. Open scene "LoadAssetBundle" and run it
7. Notice that mesh is deformed

Note: Happens due to custom shader, but couldn't find which one.
Reproduced with: 5.3.2p2, 5.4.0b5