Jazz2 doesn't automatically change black colours to transparent colours. Its more like index colour(s 0 and) 1 *are* the transparent colours. I usually take index colour 0 somewhere else (like swapping it out to some free palette entry), then make it RGB 0/0/0 (pure black). Same with index colour 1 (which is my transparent colour). I usually make it RGB 87/0/203, like Noogy did in the JCS help

Hmmm...somehow this is quite hard too explain. You just have to play around a bit. Sorry, i guess this is no help for you...btw i use PSP5, its very mighty and works fine for tilesets.