All imported Maya animations rotate whole model 90 degrees

I created an animal in Maya and created a running animation and a walking animation. For the purposes of blending animation, I created a running while turning animation on the same model without rotating it, and an animation of it bucking its head.

Now when I import the copy with the new animations and attempt to blend those animations the whole model twists, if I blend to 100% of the imported animation the model rotates 90 degrees. It also does the blended animation, blended with the original animations which aren't rotated, resulting in really messed up animations.

This doesn't only happen when I blend the animations in code, it even shows up that way in the preview window when I'm editing the blend tree. The thing that seems really odd is that these are off of the exact same model in Maya and I didn't rotate it 90 degrees after I created the skeleton or anything. I've even deleted the head bucking animation, redone it and reimported it and the twisting problem persists. I could try deleting them all and starting over, but I really don't want to lose my walking and running animation.

Does anyone know what might be causing this?

Thanks!

 

Sounds odd. Is this generic rig?
What are your root motion settings for both rig and animations? This might be where the problem lies.