I usually leave the main ISO at 200, AUTO ISO on with a minimum shutter of 1/15 and MAX ISO of 1600. That means the camera will raise the ISO to 1600 to try and maintain a 1/15 second shutter. If it reaches ISO 1600 and there still isn’t enough light to maintain the minimum shutter, then it allows the shutter to fall below that setting. If you need to raise the shutter to avoid blur then you either have to lower your f-stop (if you aren’t wide open already) or add more light to your scene (i.e. flash).
If you have the minimum shutter set to something faster like 1/60, it will start bumping the ISO once your light drops off a little, especially with slower apertures like f/5.6. What’s your minimum shutter setting at? Which lenses are you using? The consumer lenses with f/3.5-5.6 apertures are fairly slow even wide open. In falling afternoon light this combination of slower aperture and high minimum shutter could cause AUTO ISO to kick in unexpectedly.
To complicate things a little further, if the flash is on, it ignores AUTO ISO and sets the ISO to the normal ISO setting (200 in my case) and it uses the “Flash shutter speed” (custom menu e1) as the minimum shutter. I have that set to 1/30 most of the time.