This is not an Emacs bug (or a bug at all) IMO. See eg bug#766464 and its many duplicates, or the summary from bug#827639:
The problem is that you are using su to start a X/GNOME application as root. su does not clear the environment, so XDG_RUNTIME_DIR points to your users path, and the application running with root privileges changes the permissions. Please stop using su (without -l) or running X apps as root.
