What modeling app. are you using? If it's XSI, you need to make sure you freeze all your transformations (Transform > Freeze all Transforms) before you rig the model to your bones, and that goes for both the model itself and its collision model(s). If you don't, the exporter simply enters the default values for Transform, Rotate, and Scale for every object in the model, screwing everything up. I've never been able to figure out why they set the program up that way.. it's just the way things are, I'm afraid!