Try doing this:
Put a floppy disk in your floppy drive and create a floppy boot disk. (learn how to create a boot disk here:
http://www.computerhope.com/boot.htm#71 )
Now reboot your computer, and, your computer should be booting from it if the boot order is set to boot from floppy first and then harddrive.
Now try doing the chkdisk thing again.
I doubt it that it will work for three reasons:
1) I'm not really sure if a floppy bot disk has chkdisk in it...
2) If the iPod is formatted with FAT32 or FAT, then it might work...
3) I don't think that boot disks have access to usb devices.
So, this is probably not gonna work...
If you have a bootable windows xp cd then try this:
Boot from the cd, and wait until it finishes loading.
Then, press "R" to get into the recovery console.
Then try chkdisking your iPod again (don't try to chkdisk the letter that is on windows, since your device letter has probably changed here).
The windows CD has access to usb devices ... i think...
It can also chkdisk NTFS partions.
Or, try something more easier:
Boot into safemode (tap F8 before the bar that indicates that windows is loading, and select safe mode)
Then chkdisk your ipod...
/ 
