Well, the image size when making the height in gimp must be 513x513, you can change it around In-game, just go to Tools>Map Maker>World>Width, now you should see "Width" and "Height", there is two bars underneath it, you type whatever you want the size to be, in your case, 1,000x1,000.
But make sure that the size when your making the image in GIMP Is 513x513, or Feral Heart WILL crash.