I don't look at folders either, everything is set to see subfolders. So I just click the card and import.... I never look at the card. I always format (not quick format) the card in Windows and then low level format when the card goes back in the camera.
I'd submit the issue to Canon. If they can't reproduce it at the local service level, it needs to be escalated, which they do or should do. Canon also doesn't say "there's no problem" because they can't reproduce it on their service camera. They will be able to reproduce it on your camera.
How old are the cards? Or how abused have they been? As you know, there is absolutely nothing out there about this issue.
I don't see it mentioned, but it happens on both card slots?