Aqui está o que funcionou para mim:
sudo -H gedit /usr/share/applications/eclipse.desktop
atualize para:
[Desktop Entry]
Version=1.0
Name=Eclipse
Exec=env UBUNTU_MENUPROXY= eclipse
Terminal=false
Icon=/opt/eclipse/icon.xpm
Type=Application
Categories=IDE;Development
X-Ayatana-Desktop-Shortcuts=NewWindow
[NewWindow Shortcut Group]
Name=New Window
Exec=env UBUNTU_MENUPROXY= eclipse
TargetEnvironment=Unity