lol ... I had that before following your logic. However my menu doesn't get full and Gnome Commander root is not added to the menu even after a brisk lxpanelctl restart.
I was kidding about the full menu. Here it is again. This is a verbatim copy.
cat /usr/share/applications/gnome-commander.desktop
[Desktop Entry]
Encoding=UTF-8
Name=GNOME Commander root
Exec=gksu gnome-commander
Icon=gnome-commander
Terminal=false
Type=Application
Categories=GNOME;GTK;Utility;FileManager;X-MandrivaLinux-System-FileTools;
StartupNotify=true
X-GNOME-Bugzilla-Bugzilla=GNOME
X-GNOME-Bugzilla-Product=gnome-commander
X-GNOME-Bugzilla-Component=application
X-GNOME-Bugzilla-Version=1.2.8.10
X-Desktop-File-Install-Version=0.11

All I can suggest is to rename your old desktop file. Copy and paste what's shown here. Save it as the new desktop file.