A few of my collegue experiencing this before with their pendrive where all the files and fodlers in the pendrive became a list of shortcut that leads to nowherere. This a virus that actually hide all the files and folders and create a shortcut instead. I'm not too sure what its called but it has resulted in a few people having to re-type their assignments and term papers.
Some shop (that my friend send the pendrive to have it checked) resorted to a rather nasty way to remove it via formating thus resulted in the lost of all the files in the pendrive. Upon a quick search in the internet, we can easily recover the files and eliminating the shortcut files from the pendrive.
One such link is this page, fix-external-flash-drive-files-changed-to-shortcuts-virus, a very nice and step by step way to recover the file.
basically you need to go to Command Prompt (the black screen) via START - RUN - type "cmd"
and on the screen just type the following and refering it to your pendrive drive, in my example the pendrive is drive J:
the command will be as follows:
attrib -h -r -s /s /d j:*.*
give it a few seconds to execute and then walla... you'll see all your files in the pendrive again.
pretty sweet and sure beats reformating the pendrive