I don't have an iPod, but I did find a site with the answer to your problem:
http://www.gizmocafe.com/portable-audio/ipod-disc-scan.aspx
It tells us exactly how to perform a check disk on your iPod. (chk dsk is an abbreviation for check disk)
It may be preferable to first do the iPod problems check list on the Apple Computers website:
http://www.apple.com/support/ipod/five_rs/
Good luck!
