Mesh does not animate - Animator State correct, and collider animates properly

My project recently switched between a web player build to a PC standalone build. Once the build settings changed, a significant number of my animations stopped working correctly. When I click an object, I'm changing an animator parameter in order to trigger a transition. When I look at the Animator tab the parameter state changes as expected and the current clip is correct. When I look in Scene mode I can also see the collider has animated to the proper location, however, the mesh is in the original location (did not animate).

I have not been able to find a pattern. Some animations still work, while some do not.

If I switch back to a web player build, the animations start to play correctly.

I'm on Unity 4.5.0f6.

 

I completed some testing and have additional data points.
I deleted my Library/metadata folder and replaced it with a known working copy.
I deleted a prefab in my scene that was not animating properly and re-dragged it into the hierarchy.
Now the prefab animates correctly. If I made either one of the changes listed above by itself it did not work. Both changes had to be done in combination.
Is there a patch that fixes the issue? It seems like the metadata got out of whack when my build settings changed.

 

maybe the dreaded controller null for prefab that we did fix in 4.5.5p3

• (597261) - Mecanim: Fixed AnimatorController not being built properly when used in prefabs.

http://unity3d.com/unity/qa/patch-releases

 

Excuse me. Did this issue actually fixed? I may run into a similar problem in 4.6.1f1. I cannot animate material._color.a in the animation. Or, did I go wrong when entering the changed alpha value?

 

Yes this issue is fixed but it probably not related to your issue.

Can you log a bug with a small project showing your issue?

Best regards and Happy new Year