I do have a Js20th. I to have the same issue when I first got the guitar. It looks like discolored faded or something.
But someone told me it was design like that they didnt make it too shiny like the JS10th cause they had problem with the 10th annv for it being scratch easily, rubbed off easily and being chipped so often. Looks like they used a soft type paint or something.
I checked some of the JS20th in store but mostly on the net and the people that own it, and they told me that they dont look glossy or shinny.
Yes, it does look blemished they made it this way because that area should be durable for scratches from guitar pick etc. Otherwise, it may peel off easily.
Well I felt a little better knowing that all JS20th are like this.
You shouldnt try to rub it more cause it'll ruin the finish.