All I can say is that this is not upstream problem. GNOME Flashback 3.18 + Nautilus 3.14 has never been tested nor supported. If you have missing menus only in nautilus that could indicate some problem with patches in nautilus...
1) Example:
0002-Only-use-a-header-bar-in-GNOME-shell.patch
if (desktop && strstr (desktop, "GNOME")) - this is true for "GNOME-Flashback:Unity" so header bar is enabled also in flashback session, but it should not.
2) Example:
15_use-ubuntu-help.patch
if (!g_strcmp0(g_getenv("XDG_CURRENT_DESKTOP"), "Unity")) - this is false for "GNOME-Flashback:Unity", but most likely we want ubuntu help in flashback session.
Then 16_unity_new_documents.patch and ubuntu_tracker_only_on_GNOME.patch has similar if. And this is only in nautilus...
Ubuntu really should stop using "GNOME-Flashback:Unity" as XDG_CURRENT_DESKTOP... But most likely it is too late to change this for 16.04.