Can you describe where in the frequency spectrum you're hearing it? In my experience, any form of room/ambience in the tone that's anything more than short will wreck the match (as the manual mentions). Also, are you certain you're doing the match with blocks (pedal, amp, etc.) in your chain that are "close enough"?
Would be nice for you to post a clip of your source and the match side-by-side, or better yet, barring anything that makes a good match impossible, give me your source song unedited and I'll see what I come up with, and we can compare them and probably learn something through that process.