A few things to try, in order from easiest to hardest:
1) Delete from your project, then re-import it. Make sure you are left- and right- clicking on the black background at the Import screen, rather than choosing "Clear".
2) Try a different color besides black for the desired transparent background. I think black might be a special case.
3) Import into photoshop, GIMP, etc., and remove the background entirely. Save as a .png file. Then delete the existing battler from your project, re-import into the game, and if you're shown an Import screen at all, this time you DO want to use the "Clear" option on the Transparent and Semi-Transparent options.
Also, make sure you're in the correct folder when you delete and import graphics. It's possible you have the messed-up "battler" sprite saved in the Battlers folder but you're accidentally deleting/importing the correct battler sprite in the Animations folder (which is opened by default).