Same problem as Bug 47502:
the latter one is obsolete. Please remove it from the ebuild. Otherwise KDE and GNOME shows two menu entries (at least KDE).
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