Have you tried downloading the problem images a second time? If it is the reader, the issue is likely random and unlikely to impact the same image twice. Did you shot simultaneously to both the SD and CF cards? That would help tell you if it is the CF card pin or something like that.
Overall, I think you are explaining it fine and I would call Canon. Your images are being split in half with a vertical line. On the left half, the image is fine, but on the right half there is some sort of data storage issue. The thumbnail jpgs are fine, indicating that the camera is taking the image correctly, but either not storing or transferring the images correctly. This is occurring 1-2% of the time.





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