I've run into so many different problems running Tropico under X (though not the one you describe) that I don't think it's even worth trying. Even on the rare occasions when it works, it runs like molasses. I just boot back into 9 when I want to play, or better yet, don't play at all.
One problem I saw a lot, no idea how it happened, is that the game would spontaneously rename it's own libraries. Then it wouldn't launch the next time cause, surprise, couldn't find the libraries. You might check out that one...