
There's a lot of people having trouble with this. The problem is that you're missing -jpgtga flag (Enable jpg/tga textures) in Launcher. So a lot of ships mapped with these format bitmaps are going to be invisible.
In recent future, -jpgtga flag is going to be removed from next builds. It's going to be on by default. (In fact, some betas have done it).
Remember to enjoy the game and to avoid asking about a game starting with FS and finishing in the first odd prime number

(It can drive some people mad

).
I would also recommend you to stop playing FS2, go to
Freespace Conversion thread, download fsport. And then start playing FS1

within FS2 engine. Then move to FS2 main story.