Hi Cleon,
I don't know the Canon program too much, but I understand it doesn't provide true raw data. Correct me if I'm wrong, but I think the Canon program always subtracts the dark pedestal and applies a white balance correction, and I think it also interpolates the data to de-Bayer the image.
To work with DSLR raw images, you must set DSLR_RAW preferences as follows:
- Color Adjustment: all values = 1.
- White balance: both options disabled.
- Either "Create RAW Bayer" or "Create RAW Bayer CFA" enabled.
- "No black point correction" enabled.
With these options, you'll be reading true raw pixel data as it has been stored in the device. Let me know how it works this way.