There could be a thousand things that could be going on here, could you describe your model in more detail? How many meshes make up the model?
As long as your model isn't animated or have a linked heirarchy, it would be best to combine everything into a single mesh, then collapse your modifier stack before exporting.
And one other thing that can wreak havok and cause you to pull out your hair: I always use the "Reset XForm" function before exporting. Its in the utilities tab on the command panel. If you've applied a lot of transforms to your model (scaling, moving verts, etc.) then this resets everything to a default state. If you don't, this can REALLY scrw up things in the game engine with collision and other things, especially if the model is animated. But its good practice to do this regardless.