You can set somewhere in GIMP the background color transparent, so it shouldn't turn black. (I don't know exactly where, since I don't use GIMP myself :< ) Alternatively you can bucket the background to some color (bright aqua or pink, whatever you want) before scaling. The black pixels belonging to sprite don't that way mix with the black background, if you don't find a way to get rid of the background appearing. :3
The background color doesn't matter, since in editor, you can pick that as transparent color. Just need to make sure that color doesn't appear in sprite, or you get some transparent pixels in there.
I hope I understood right your newer problem. : o