Comment 5 for bug 869326

I had the exact same problem and the workaround I found which works perfectly is to uninstall the global menu functionality in Unity as it is that option that causes gnome-terminal to display a menu even if it is asked not to.
To uninstall unity's global menu: sudo apt-get remove appmenu-gtk3 appmenu-gtk appmenu-qt
I don't know if it is required to currently use Unity for changes to apply correctly, but I re-logged my account on unity to execute the above command then returned to gnome shell and it was fixed.