You may need to get Blender to center the ship and recalculate the object's center so both the center of the object reads 0,0,0 and that center is positioned at 0,0,0. I don't use Blender, so I don't know how to do that using it.

This tutorial may help you do that: https://blender.stackexchange.com/questions/1291/change-pivot-or-local-origin-of-an-object