I've sometimes had a problem with saving the image in wrong .tga type. It has to be RLE packed, and something else. I circumvent this by saving the final image with IrfanView, which makes black transparent as it should be.
You can just make the black background 100% transparent; that works just as well.
Well, it's not the RLE... I'd really hate to go around and erase the black but that might just be the easiest thing at this point (lots of details I'm going to have to go around.)