Canon stores many forms of ISO information. Basically, what you want to use is the composite ISO value which should be accurate no matter what mode your camera is in.

The CameraISO gives the camera setting, but this isn't available for all models.

The BaseISO and AutoISO combine to give the ISO that was used for taking the picture, with the formula ISO = BaseISO * AutoISO / 100.

I'm not sure why Canon does it this way, but I'm sure they have their reasons.

I hope this helps.

- Phil