Ugh,,, This... I know this all too well. When it does this, try deleting one of the duplicates, When this happens to me, one of the duplicate songs/albums will either delete when you hit the <Del> key or it will stay. remember which one it is (either the first or second) because it will be the same one for all of them. As of now, I don't know of a way to keep it from doing that, so just do the same thing if/when it happens.
Hope that helps.