I don't think that Dark Messenger is the same as Kuja's theme as I have the two different songs on my comp. Dark Messenger is played during one of the final battles (SPOILER) with Trance Kuja. It's more upbeat and rock-ish. Kuja's theme... I can't remember where it's played but it's sort of more piano, kinda slower and mournful.
Someone correct me if I'm wrong ^^ I hope to get the cd soon for the soundtrack (when I save up £34!)