This has not been resolved in Unity 5.4.

I'm still having this issue on Unity 5.4.1f1, I tried the workaround suggested by OMAR_UNITY, but no luck with it.
Since this is a problem that only happens on the editor for me, one workaround that worked was to add some lines of code only for when in the editor, where the asset loaded from AB would have its shader re-set by its name:

#if UNITY_EDITOR
foreach(Material material in [rendererLoadedAssetBundle].materials)
{
material.shader = Shader.Find(material.shader.name);
}
#endif

Maybe this issue is related to the fact that almost the same thing happens with sound sources loaded from asset bundles in the editor. They are loaded without errors, but their references to the audio mixer groups are broken, even though the naming of the references looks correct.

This is not resolved. Still exists in 5.4.1f1

This is not fixed in 5.4....

Still there in Unity 5.4.1p2. I still need to reassign all custom shaders after loading an AssetBundle with WWW. I built the AssetBundles in the OSX Editor and when I test the built game, the shaders are not loaded. The same project in a Windows Unity3D 5.4.1p2 editor shows the same problem. I can reassign the shader by hand and then all the other objects which are using the same custom shader are fixed at once. :-(

i have exported the assetbundle(.Unity3d) from Unity5.3.5, when i import into the file in Unity5.4 pink color is coming. But in texture i have my textures and all the details.
How do i solve this issue?
I cannot reexport all my assetbundle again from Unity5.4

This is not resolved. Still exists in 5.4.0f3

Hi, this issue still happen in Unity 5.4.0f3 the last version.
I'm using this BuildPipeline.BuildAssetBundles(pathTemp, BuildAssetBundleOptions.None, BuildTarget.StandaloneOSXUniversal);

When I use the bundler I have lost shader references than be see in the typical pink color.

And I have to make a "hack" :

//************ HACK ! still unfixed >.<' https://issuetracker.unity3d.com/issues/materials-lose-reference-to-textures-if-loaded-from-asset-bundles?page=2#comments
Renderer[] renderers = imagesToLoad[i].GetComponentsInChildren<Renderer>();
Material[] materials;
string[] shaders;

foreach (var rend in renderers)
{
materials = rend.sharedMaterials;
shaders = new string[materials.Length];

for (int i2 = 0; i2 < materials.Length; i2++)
{
shaders[i2] = materials[i2].shader.name;
}

for (int i2 = 0; i2 < materials.Length; i2++)
{
materials[i2].shader = Shader.Find(shaders[i2]);
}
}

5.3.1f1 has this issue ,when I load level from asssetbundles ,this scene lose ligntmaps,woe need reapply shaders.