At one time I owned a '97 Roadking with a two tone paint job. This was before the RKC came out. I had the nostalgic lid rails which mounted on top of the lids. I also had the nostalgic bag rails that went around the side of the bag. If the later is what you are referring to???? I don't remember as such that they raised upward. However I do remember this. A lower portion of the bag was painted black the upper majority of the bag was the mystic green metallic. There was a pinstriping separating the two different colors. Getting to the point here: The chrome side bag rails and the paint line which separated this two colors did not run level with each other. Which I thought was rather distasteful although it seemed like both of these "straight" lines were level. It was one of those things that I noticed but nobody else ever noticed it or said anything about it at any rate.
You may have a defective item and if that is the case (if you can) take it back immediately and demand a replacement. The dealer I deal with would have no problem exchanging something like that. Hope this helps some.