Just checking to be sure, but is the tempo of your song and the Real Track you're trying to use compatible? Generally speaking you get some wicked artifacts if you go too far outside the intended tempo range of the Real Track. The slower the tempo the more noticeable it is when trying to add a RT with a faster tempo. That's not always the case but I've found it to be so more often than not. When you say out of tune or discordant, that's what it makes me think.