Either this is a bug or I'm missing something, but when you put glass on the bottom and the dye on the top, you get black glass. There's also the thing where it seems to work with anything with the colour in the name, rather than just the dye itself... So I made cyan stained glass with cyan stained glass. Actually, it seems to work with anything, just if the combination doesn't work, it makes black glass, regardless of what's in... And then I got pink glass from cyan wool and cyan wool... I think something's a bit funky here.