Same problem as Bug 47502: /usr/share/applications/skype.desktop /usr/share/applnk/Network/skype.desktop the latter one is obsolete. Please remove it from the ebuild. Otherwise KDE and GNOME shows two menu entries (at least KDE). Reproducible: Always Steps to Reproduce:
The ebuild uses eutils make_desktop_entry so this is not a skype ebuild bug, maybe a eutils one? I do not use gnome or kde so i cannot see. make_desktop_entry skype "Skype VoIP" ../icons/hicolor/48x48/apps/skype.png