I've had this problem while operating on 2 different file paths.
The first time this happened, I was ingesting from cards using Lightroom. LR was creating an automatic backup to a separate drive. The image was imported into LR, and not touched by any other software. The image and
the automatic backup images were both corrupt (and in the same way).
Sometimes, for the sake of speed, I'll also download directly off the card (using Mac "image capture"), make backups from that, and do an initial edit in Photo Mechanic. In photo mechanic, the files do not show the corruption, but upon import into LR, they do show the corruption. The backup of the files (which have never been touched by LR, but I try to open with Photoshop or the Canon utility) also exhibit this issue.
A recent addition to my system has been an additional CF card reader (FW 800).. and for awhile I was completely convinced that importing the images simultaneously was somehow causing the issue. But then I realized that I saw this issue at least once before I got the new card reader (I compared the EXIF data to my b&h receipt
Also, don't know if this could be suspect, but I am using a Norco eSata enclosure. I've had it for a year+, and haven't had any other issues, but is that something I should be looking into?
I've removed the suspect USB card reader from the system, and I'm going to keep my eyes open to see if the problems recur.
Another couple questions in the meantime while I try to work this out: Is there any way to check folders of files to see if they might have suffered this sort of corruption (for example, that's what I was hoping that Image Verifier would do... is there any other software I should check out?). Also, thank goodness that this problem hasn't affected any truly critical files, but is there anything I could do to try to recover such a corrupted file in the future?