Because this is kind of weird to explain, let's show you what I mean. This is in my game. When I import this base ship model, it should be at (1000,1000,1000), but the model acts like it's at (1000,1000, 0). Note it is positioned correctly when I use a .x model. So it has to be the model. I need to know what's wrong with it.
Here is the model file, tell me if anything is wrong with it: https://dl.dropbox.com/u/92848165/station2.FBX
EDIT: The model works if you import it into Google Sketchup...but you lose the textures, not very nice.