How to solve weird Mecanim and Bootcamp rotation problems?

Hey, I want to use the bootcamp model for an AI showcase in my game, my problem is once I set it up in mecanim and make an animation controller using it's OWN animations they all work well, except the crouch and reload ones. This is what happens, the animation when tested with the soldier model is rotated in the X axis by 90 degrees and the rotation offset only modifies Y. So when I play it, the soldier just transitions to say a 90 degrees rotated position... looking down. The weird thing is, if I retarget the animation to any other thing, say the Mecanim Example character, the reload and all other animations work perfectly fine, without the rotation. I've already tried Bake Into Pose and nothing, and this only happens with the Bootcamp model and it's own animations. Using other models or the legacy anim system it works fine, but how can I solve this. And one quick question, how can I import the animation so I don't enable it to move the root in X and Z axis, but just in the Y? Thanks