skeleton.ms3d not working with default animations

I have all the verts assigned like they should be, everything is setup as it should be, but in game I have two wierd things:
1. the player's head is removed and floating above the player. (body is one mesh, then the head and helmet are separate, verts are welded though)
2. The body is fine in root, but when you move, the legs jerk out of whack really bad. (Has done this on multiple models)

I really don't want to go through and make all the animations again. Any ideas? exporting incorrectly?

Thanks,
J