Why does this happen?
 

....

What?

I think he's referring to the color black being made transparent...just change all black [RGB: 0,0,0] to something else like [RGB: 1,1,1 or 5,5,5]. That's what I do and it usually works

Graal handles pure black and white as transparent. It's a dated technique and I wish Stefan would remove it but he doesn't seem too keen on it -_-