I have same problems I had since first install of WordPress 3.6 on Debian 7: themes and plugins are installed under directory:
but most of them have to manually moved to:
and symlinked from the first to the second location to work.
Then, when I have to update them, I have to move them back to first location (after deleting the symlink), to do the update, to move to the second location and to do the symlink again.
For sure there is a better way to do it and this is due to something I configured badly, but I don't know what.