Comment 17 for bug 1436297

No I don't have any nautilus related files in ~/.local/share/applications/

I think Colin pointed out (in the duplicate bug) that the problem really stems from the fact that in /usr/share/applications, there's nautilus.desktop and then there's org.gnome.Nautilus.desktop, which is marked with NoDisplay=true.

Seems like the one in the Application menus is nautilus.desktop, but the one that gets launched is org.gnome.Nautilus.desktop, so the windows aren't properly matched to the icon.

org.gnome.Nautilus.desktop also doesn't have any of the right-click menu bookmarks.

Is it possible to get rid of nautilus.desktop, mark org.gnome.Nautilus.desktop to appear in the menus, and then associate the bookmarks to it?