Quote Originally Posted by gbc View Post
Shot another 900 or so shots tonight, with a new Lexar CF card that I used two nights ago with no problems. Downloaded the files straight from the camera via USB. Tonight, about 15 shots had the same discoloration problem. Starting to worry the problem is in the camera and not the card and/or reader. Any ideas what could be causing it? Not even sure how to describe the problem to a Canon repair center without showing them a picture.
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As others have suggested, you should do more troubleshooting to isolate it. Shoot to the SD card first and see if happens there. Shoot to both and see if it's specific to one type of card. Shoot RAW+JPEG and see if it happens in both types.

If it's not specific to one card, it's either the camera's main board or the card reader socket in the camera. In the end, the cause doesn't matter: document the troubleshooting you've done so far, print one of the pictures so Canon can see the results, and send it in for repair. They have so many tools at their disposal that it's just not your responsibility to diagnose the problem; let them do their magic and get you back in business.