It sounds like you aren't rigging your model properly. I would check to make sure your model is parented to the right bones, and then you can enter pose mode with the armature selected to test to see if it was correctly attached (in pose mode you can move around the bones and see if your model follows it). If it does, then you should be able to export correctly... also make sure that when you compile using the in-game compiler that you use a different file name each time. As far as I can recall, the importer is bugged and won't update the model if you use the same name.

I still can't get it to line up right, can I add you on skype if you have some time and go over this with me?