Don't know if this is it, but I noticed a couple weeks ago the tail piece on my '04 is sagging downward a bit, making it appear the rear end of the seat is sitting up a bit higher than it really is. I bungee stuff down to the rear seat (never have the cowl on there) all the time, including stuff resting on the tail piece behind the end of the seat, so I guess I'm not surprised this happened. Not thrilled about it, but it doesn't seem to be a problem. Check your tail piece by putting your hand on the taillight and gently lifting it straight upward. If you have more than a few mm. of movement you might have the same issue I do.
I checked the tailpiece but there's no sag at all. Popular consensus seems the top rack's bracket area's the cause. Since they are rubber coated I'm gonna try Randy's idea and trim them, hopefully without messing up the weather seal or the tail piece. Comments, warnings, threats, promises of riches unknown?
Go get yourself a tube of epoxy type paint to put over the portion you trimed off. That should seal it up nice so it wont rust or weather.