One additional thought, maybe the camera is changing the ISO but not showing the change in the viewfinder. What does the simulated exposure meter show as you change the exposure? Does it continue to show proper exposure or does it indicate an improper exposure in the amount that you have changed the aperture or shutter speed?
If you take a series of images in Manual with Auto ISO, do the histograms look similar or do they indicate changing exposures? What about the resulting images, do they look about the same, or do the show changing exposures?
What ISO is shown in the meta data of the image? You should be able to view this in the optional image playback displays in the camera and with most post processing programs.
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