I may have cleared it up. I've had it for... as long as I've had Wacup, which is almost a year I guess. Anyway, I switched skins multiple times today and trying the same skin again, it seems to be gone. After some playback, it came back. So if I switch skins, and return to this one, it goes away. I'm now convinced the ghost seek bar is what's bugged, specifically.
Update: I have more info. It seems it sometimes begins to separate both seek bars when I use Global Hotkeys to skip through a song. But it doesn't begin having a second ghost bar every time. Once it does, it is there to stay until I switch the skin back.