Don't use so installed eclipse.(I'm on 13.04)
opens the .desktop file which shows...
gksudo gedit /usr/share/applications/eclipse.desktop
Launcher works fine.
Comment=Eclipse Integrated Development Environment
If I start eclipse in terminal with /usr/bin/eclipse or with the launcher
System monitor shows the start commands full path to be...
Test that in terminal and edit the .desktop file if it works. ...