This probably means you have oriented your ship models incorrectly in your modelling software.
To use XSI as an example, but I believe it is the same for any modelling software which uses the standard 4 perspectives (usually Top, Front, Right and Isometric), you have to orient your model so that when the model is viewed from the Top perspective, its front end is pointing down.
When I imported my first test cube into the game I had that same problem, and the above fixed it.