In your FL directory "C:\Program Files\Microsoft Games\Freelancer\DATA\INTERFACE\INTRO\IMAGES" you'll see 3 .TGA files.
startupscreen.tga 800x600 24bit TGA (no alpha)
startupscreen_1280.tga 1280x960 24bit TGA (no alpha)
front_freelancerlogo.tga 800x600 32bit TGA
The first one is what most people will see, the second is for those on a screen res of 1280 or higher and the last is for the menu screen.
Most Paint progs that can do TGA formats will handle the first 2, but you need one that can handle transparencies as well as alpha channels for the the third, as the whole thing is done in the alpha channel rather then the RGB channels.
**shuffles of with a new headache**