Have you tried connecting both via display port or both via HDMI?
Not that that should matter normally, but good starting point in trying to get around what may be a bug?
Edit: just remembered I've been having intermitten problems with my 2nd display since last nvidia driver if I have my vr head set plugged in to the 3rd port (even off). When i unplugged it and restarted I got my desktop loading as normal.