I've noticed it also seems to come from the sky too rather than the Dragon. But then sometimes it comes directly from the Dragon's head. Maybe it ends up spawning too high in the air and immediately despawns?
Dragon fireballs seem to be shot from the mouth. I looked at it from a third person view in 15w35a, and can confirm it gets shot out of the mouth. This issue seems to be resolved. Mod please close.
The problem is the Ender Dragon is capable of destroying its fireball on contact. Therefore when the fireball is fired, it often spawns inside of the dragon and instantly gets destroyed.
I've never experienced it being invisible for me. What usually happens to me is that the fireball simply never appears, or after I hear the firing sound, it comes down from the sky seconds later.
I also want to add something. I'm not sure if this is still an issue, but when I fight the dragon, it seems like sometime the fireball appears over me, not from the dragon. Sometimes it will even be super close.
It would make sense for it to be a feature, so that the chnaces of the dragon destroying it are smaller. But why do that when you could just make the Ender Dragon not harm the acid? Thats what makes me think its a bug, but I don't know.
The way I test it is just run around the end until the dragon shoots (the sound is played) and a fireball is no where to be seen. It's random from what I observed. I'll test it and update it later; out currently.
Can confirm