Hi! Maxy and I have been trying to reproduce this problem using nemo and nautilus both from unstable and stable and we have not been able to reproduce this.
The nemo-autostart.desktop file is only installed in /usr/share/applications. In cinnamon, it's started as part of cinnamon session, but given that it's not part of /etc/xdg/autostart, it shouldn't get autostarted by default. Stephen, could it be that you had nemo-autostart as part of /etc/xdg/autostart? Or that you had added it to your local ~/.config/autostart directory? -- Regards, Marga