This may be completely unrelated, but I recall some issues with KS level editor appeared when the path was too long. In other words, try moving the KS directory to the root directory, e.g. C:\Knytt Stories\, and see if the problem persists.
Also, when reinstalling, did you simply extract the game files into the same folder as before? And the KS editor still gives you the same mistake? If yes, try extracting to a completely new folder and trying the editor again, because KS automatically incorporates whatever levels it finds in Worlds. If the editor works, you can simply copy all of the levels you want to keep to the new Worlds folder - just take care to not copy any potentially problematic levels, i.e. folders with strange names
And finally, the only time I had a () level listed by the game, it didn't appear that way in the Worlds folder. It appeared as a normal [author] - [level name] folder; the problem was in the world.ini file.