High ISO in D800 when Auto ISO turned on

I have take a number of shots in my house during the day, cloudy but still decent light. The Auto ISO was turned on and set at 100/6,400/Auto shutter speed. The pictures all had fairly high ISO, in the thousands. I would have thought it would select values in the 100's instead? Also, when I use the pop-up flash the ISO jumps up tremendously. For example, a shot in a well lit room would have ISO 250 or 400 with the flash off, but go up to 1,600 with the flash on. This seems counterintuitive?