Ok, let me phrase your question a different way.

"I can't find how to get anything transparent. By the way, black is transparent."

The purple color is only transparent in JCS. For the actual image, use 0,0,0 (actually, the two colors on the top left of your palette are the transparent ones, but 0,0,0 is usually one, if not both of them) for the transparent color. For non-transparent black, use something Close to that, such as one of the darkest shades of the sprite colors.