Batching animations - Combined Skin Mesh script disappearing help

Hey guys, I am trying to optimize my mobile game (for iPhone 4).

I will basically have tons of animation on screen and trying the best way to batch them.

The animations have bones/skin mesh renderer on them. I understand this will cause the animation to not dynamically batch.

So I tried using a Combined Skinned Mesh script here: http://wiki.unity3d.com/index.php?title=CombineSkinnedMeshes http://wiki.unity3d.com/index.php?title=SkinMeshCombineUtility

I think I get it working as drawcalls stay very low with many animated objects, however the animation is never in the right place and I can't figure out why? Does anyone have any suggestions on how to fix this problem?