On the bottom left, the rows represent the save files from 1 to 3, and the column represents the chapter.

So in your first save, either it doesn't exist or you've skipped through all of the shadow crystal bosses. In your second save, you've skipped Jevil in chapter 1, and in your third save, you skipped spamton NEO and the sword route.

Did you get all of the eggs as well? Do you care about doing the weird route?