- In order to validate the DVD, X-Plane decompresses part of its contents into the preferences folder. Why preferences? There is no good reason - it's historic.
- X-Plane will create a preferences folder if there is not one. But it does not do that until you quit.
- The X-Plane installer will not make directories unless they contain files.
The next patch of the sim will fix this, but in the meantime, if you delete your preferences, leave the empty directory in place!