Null inspector values when using scene assetbundles with unity 5.4.0f3


I have a working project that worked fine on Unity < 5.3 without problems. The project contains asset bundles that contains only one scene (automatically all referenced stuff in the scene should be included in the asset bundle).
It just worked fine before, until I upgraded to 5.4.0f3 because I am using custom REST Api and wanted to use the new Unity Networking.
First problem I encountered is this error.
‘LoadAllAssets function no longer works on scene asset bundles’, so I removed the LoadAllAssets call, and just loaded the scene, which works, but with the following hair pulling problem.

Things that are set in the inspector are null

If I set in the inspector a reference for a prefab, or another object/component in scene, it ends up null in code. I didn’t understand why the game is not running correctly, but when I debugged it, I found the null exceptions everywhere. I am not sure if every single inspector reference is null, but the null references are enough to break the game completely.
I can’t revert back to older unity because I’ve built a huge stuff based on the new Networking, so I really need a workaround this.
I did run-time stuff like below as a work around, but this cannot be done for prefabs.

PointSound = GetComponents<AudioSource>()[0];

Any help is greatly appreciated

I had this public serialized GUIStyle which was causing the problem only in 5.4, it was not causing a problem before.

public GUIStyle ScoreStyle;

Changing it to non-serialized solved the problem. It sounds like a unity bug to me.

GUIStyle ScoreStyle;