I am of the same opinion with philinux regarding "gksu nautilus".
Also, I very often "clean" folders and files or edit them with gksu nautilus and then with gedit.
Believe me, it is a useuful command.
Anyway we need an explanation why this is not working anymore.
Downgrading to the version 3.5.2 solves this issue anyway for now.
I am of the same opinion with philinux regarding "gksu nautilus".
Also, I very often "clean" folders and files or edit them with gksu nautilus and then with gedit.
Believe me, it is a useuful command.
Anyway we need an explanation why this is not working anymore.
Downgrading to the version 3.5.2 solves this issue anyway for now.