It could be something to do with the Disk Utility. Disk Utility is designed to erase disk drives and external hard drives. It could be erasing the files when you eject. I never use Disk Utility, just copy the files from the finder however I just did a test mounting my Hama card reader. Disk Utility shows the details of the card and a sub folder but not the reader. I hit eject and put back into my 5D and the files are still there. I used the same card as you on a 5D Mk II.