This is going to sound stupid but.....

[Hellraiser]

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?

[Ice M A N]

"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

[JelZe GoldRabbit]

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 :)

[EvilMike]

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.