The Animation editor still has a few bugs I'm afraid.

jemplode is forcing black in areas wear it thinks there are no pixels, that way jemplode does not have to write the extra info to the player. jemplode also still treats frames which are identical within the animation as duplicate frames and will not upload them. If you make a change to one of those "duplicate" frames, all other duplicate frames change as well.

Open up this animation and you will see what I mean.