Thanks for the samples. It is true, the reported ISO is wrong in the Auto and Auto-High settings (always reports 100). There are a couple of interesting unknown values, but I can't correlate either of them with the ISO's that I calculate for the images across the different samples.
Below is the information I get from the images. Pictures IMG_0535.jpg - IMG_0541.jpg and IMG_7005.jpg - IMG_7007.jpg are two series that (I'm assuming) were shot under the same lighting conditions.
I've added decoding of the "Auto High" setting. The 0x0001 information is interesting, but unfortunately is 0 for one of the Auto shots, so I don't think this can give us what we want. 0x0003 seems to vary depending on the ISO, but is different under different lighting conditions, so couldn't be decoded to ISO per se.
So at first look, I can't see a place where the ISO is stored in Auto or AutoHigh mode.
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Users/phil/Desktop/S3IS Samples/IMG_0526.JPG
ISO : 100
Camera ISO : Auto High
Aperture : 2.7
Exposure Time : 1/250
Canon Shot Info 0x0001 : 64
Canon Shot Info 0x0003 : 145
======== Users/phil/Desktop/S3IS Samples/IMG_0535.JPG
ISO : 100
Camera ISO : Auto
Aperture : 2.7
Exposure Time : 1/30
Canon Shot Info 0x0001 : 0
Canon Shot Info 0x0003 : 122
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Users/phil/Desktop/S3IS Samples/IMG_0536.JPG
ISO : 100
Camera ISO : 100
Aperture : 2.7
Exposure Time : 1/30
Canon Shot Info 0x0001 : 0
Canon Shot Info 0x0003 : 122
======== Users/phil/Desktop/S3IS Samples/IMG_0537.JPG
ISO : 200
Camera ISO : 200
Aperture : 2.7
Exposure Time : 1/60
Canon Shot Info 0x0001 : 0
Canon Shot Info 0x0003 : 113
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Users/phil/Desktop/S3IS Samples/IMG_0539.JPG
ISO : 400
Camera ISO : 400
Aperture : 2.7
Exposure Time : 1/125
Canon Shot Info 0x0001 : 0
Canon Shot Info 0x0003 : 117
======== Users/phil/Desktop/S3IS Samples/IMG_0540.JPG
ISO : 800
Camera ISO : 800
Aperture : 2.7
Exposure Time : 1/200
Canon Shot Info 0x0001 : 0
Canon Shot Info 0x0003 : 111
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Users/phil/Desktop/S3IS Samples/IMG_0541.JPG
ISO : 100
Camera ISO : Auto High
Aperture : 2.7
Exposure Time : 1/125
Canon Shot Info 0x0001 : 64
Canon Shot Info 0x0003 : 115
======== Users/phil/Desktop/S3IS Samples/IMG_7005.JPG
ISO : 100
Camera ISO : Auto
Aperture : 3.5
Exposure Time : 1/30
Canon Shot Info 0x0001 : 32
Canon Shot Info 0x0003 : 96
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Users/phil/Desktop/S3IS Samples/IMG_7006.JPG
ISO : 100
Camera ISO : Auto High
Aperture : 3.5
Exposure Time : 1/160
Canon Shot Info 0x0001 : 96
Canon Shot Info 0x0003 : 101
======== Users/phil/Desktop/S3IS Samples/IMG_7007.JPG
ISO : 79
Camera ISO : 80
Aperture : 3.5
Exposure Time : 1/13
Canon Shot Info 0x0001 : 0
Canon Shot Info 0x0003 : 100