I've been trying to recreate this problem with USB LoaderGX for months with no luck.
@OP can you give us any other info on how this happened? What game were you attempting to load? What version of USB LoaderGX were you using? When you say "I went to save the config file" do you mean the game load settings? Have you recently changed the format on your hard drive? Any additional info you can think of would be appreciated as we would really would like to get to the bottom of this.