Comment 5 for bug 739454

Another interesting observation: in a unity live session, if I remove the nautilus home icon from the favorites (uncheck "Keep In Launcher"), then log out and log in again, new nautilus windows will be matched against "nautilus.desktop", not "nautilus-home.desktop".

So it looks like the way the list of favorites is built when the launcher is started influences how bamf matches applications to desktop files.