I've had this problem with JCS. Whenever I try to build one of my images into a tileset, the tileset itself after it has been built, has no black!!!! all the black in the tileset turns into the invisible key! is there any way to prevent this?

"Doctor, it hurts when I do this"
"Then don't do that"

Use something really close to black, but not quite black. Er.. that's what I always do anyway. :P

Real black, as in R=0, G=0 and B=0 cannot be seen by JCS or JJ2. So use a color real close to black. like, R=1, G=1 and B=1

Actually, I find that you need to have something around #050505 at the least in order for the colour to show right. I have tried "almost black" things like #010000 but those seem to be a tad glitchy.