Did you set the Auto ISO limit at 4000? I didn't see anyone ask this question.
Maximum auto ISO limit was 12800. I think I managed to prove that whole point about camera not selecting ISO values above was limit in metering system. In this case exposure value was EV -3 (1.6s, F2.8, ISO 4000). With F4 lens that limit was EV -2 and with F1.4 lens limit was EV -5. So it seemed that limit for camera metering was EV -6 with theoretical F1.0 lens and less with dimmer lenses. Each stop of lens brightness drops maximum meterable exposuer by one stop.
Reference for calculation of exposure value: