If you are using USB and external drives then do the following

Download MCShield to your desktop and install
It will initially run a scan and show the result as a toaster by the system clock
Then in the control centre select scanner and tick unhide items on flash drives

https://dl.dropbox.com/u/73555776/mcshield%20unhide.JPG

Plug in the drive and McShield will start a scan

Then get the log which will be located under the logs tab on the main page

And post that