Steps to reproduce:
1. Open User's attached project
2. Open scene "testImportAssetBundleFrom5_3_4"
3. In the editor menu, select the "Scale1Portal->Load->Load an Asset Bundle" tool
4. Select the "boeing737" bundle from the Assets/BundleToImport folder of the project

Result: standard material that was assigned to all parts of the game object is lost.

Reproduced with: 5.6.0b1, 5.5.0p1, 5.4.2f2
Not reproduced with: 5.3.6p4

Walkaround: Manually changing all the empty shaders to the Standard Material shader gets back the proper materials.