You can also compare this to the output of df -h, which reports filesystem usage. From that directory, also try du -h to see the sizes of the files/directories on the drive. Then cd to the USB drive (usually a subdirectory in /media/), and run the command ls -a. On Linux, open the terminal and login as root or run sudo bash.
Did the files/folders get marked as hidden, or are they simply unreadable to the user accounts you're using?
