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.

 

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?