Ugh, red text on a black backround...really hard to read your post.

I found a bug today in the save game code.  The save game code attemps to copy your shipcfg files into the save game file so that it can re-create the shipcfg file if you move the save game to another computer, delete your ships folder, etc.  If it failed to open the file, and I'm not sure why it would, it didn't handle the error correctly and ended up messing up the save game.  I think that I've fixed it here, but I haven't had a shipcfg file fail to open.

You might be able to prevent the problem by deleting the ships that your custom race uses (or your whole ships folder to be safe) so that you're playing with new ship designs.