Don't know if this will help but.....
I once got a similar problem. I loaded the .emp files once I started a game and any old shipset would show up, not the one specified in the .emp file. This was the problem, I was using the TDM-Modpack, but all the races I had installed were in the basic se4 pictures/races folder not the TDM-Modpack pictures/races folder so the Path.txt pointed toward the TDM files for it to look and se4 could not find the pictures because they did not exist.
Make sure your Path.txt points towards where the .emp file is looking if you are using some kind of modd.(ie if using TDM-Modpack then the path must state 'TDM-Modpack' instead of 'None' in the Path.txt, just open with notepad and edit manually)
If the above does not apply to you.....then just ignore an old mans rambling at 5:06am
