I have used fsck.vfat /dev/hda3 on my C3100 running Cacko several times.
My partition is 3.8GB (Default Sharp/Cacko partition)
My only complaint about this is, It only works in emergency mode, using the D+B option.
I think I get a similar error as daneil3000 if NOT using emergency console.
A year and several months ago I when I first got my C3100, I was having a problem with a file that "seemed" like it wasn't completely deleted.
Someone that knew what they were talking about, told me to use this after starting emergency mode with the D+B option.
To do a file system check on /hdd3 use below command:
If you boot with the B+D option, login as root and use
fsck.vfat -a -f -t -v -V /dev/hda3
This has worked for me every time.
It does take about an hour or more to finish.
It does warn that FAT32 support is ALPHA
BTW, checking a drive or defragging a drive over USB in Windows is very slow. I don't recommend this.