I think your problem comes from the scaling part.
You have to figure out what size to make your model initially in the 3D modeling program of your choice so that when you import it, no scaling is required. It's the scaling of the bones that makes it go all wonky if I'm not mistaken. My wife's a pro animator for EA. She was just talking about this the other day. If that doesn't help, I can try and get some more specifics.
She also mentioned just baking all the animation and export it all as vertex animation, since that's what the engine seems to prefer. But if you want more than one, you have to deal with additive blending.