Normally this can only be caused by renaming one of these folders. Technically the default X-Plane packages are the same as any other package. That is why XO relies on the name to recognize them. So, giving these packages back their default name will solves this.
Sometimes people order their scenery by renaming and prefixing the packages, but this is of course not needed when using XO.
It is also important to realize that the X-Plane installer will automatically reinstall the default packages when updating, because it thinks that they are missing and you end up with duplicate scenery. Renaming default packages is therefore not a good idea.