When you change the world folder to go to a different directory, for instance set it up like this:

world: ../Server (Spigot 1.9) Worlds/Survival

In this case "Survival is the world, but the directory has been changed from the normal server directory to the "Server (Spigot 1.9) Worlds" directory.

This all works great, but some permissions get into trouble with localizing the world once the directory is changed.

For instance:
PermissionsEx can do global prefixes and suffixes, but it cant do per world permissions.
(You can read more about that over here: https://github.com/PEXPlugins/PermissionsEx/issues/2348)