I had a very similar problem to yours. Here is my problem and solution
from some months ago.

===========Old Problem letter===================================

My / partition is filled, but the amount of data in it is minimal, to wit:
 
/dev/hda1             3.7G  3.6G     0 100% /
/dev/hda3             1.4G  1.1G  216M  84% /mnt/hda3
/dev/hda4              22G   17G  4.0G  81% /mnt/hda4
/dev/hdb1              27G   18G  7.9G  69% /mnt/hdb1
/dev/hdc1              71G   46G   21G  68% /mnt/hdc1
 
[root@jhammer6 /]# du -sh auto bin boot dev etc initrd install lib lost+found root 
sbin shlib test
tmp
2.0k    auto
5.9M    bin
3.3M    boot
15k     dev
3.6M    etc
1.0k    initrd
11k     install
44M     lib
12k     lost+found
46M     root
6.2M    sbin
208k    shlib
7.0k    test
80M     tmp
So, du reports less than 200 M bytes but df reports 3.6 gigs in use.
Obviously, I do not have gigs of data on the root partition.          
============End Old Problem letter=================================

I finally answered my own question.

==================Old Solution letter==========================================
I finally found out where my hard drive memory was going to on my root
drive /. (Or, I may have rediscovered where those missing bytes are. Ain't
it nice to mature.)
 
I have a root hard drive with about 3 gigs of space on it. It got filled
up even though I have moved almost everything off it. Very puzzling.
 
Turns out, I have a mnt point for a backupdrive, /mnt/hdc1, on the root
drive. This backup is automatic. If the backup drive isn't mounted, the
backup program, cp -au, just merrily makes a directory /mnt/hdc1 on my
root drive /, and writes to it, thus filling up the / drive eventually.
 
This is a tough thing to find out because if you mount the backup drive,
which is the default configuration, you don't see the extra directory
/mnt/hdc1.
 
Well, lucky I usually keep an extra OS on my system, so I can boot into
it and play around with my usual / directory.  (Now, where will I use
that 80 gig drive I just bought to replace my old "defective" hard drive.)

====================End of old Solution letter===================================

Isn't it nice using just text email (mutt) so it is simple to keep and
search old email?

Joel

                                                                                
On Tue, Nov 26, 2002 at 08:56:26PM -0600, Alan Jackson wrote:
> I'm at my wit's end. A runaway vim process filled up my disk, and I can't
> figure out *where*. I had cleared space a few days ago, and then it filled up
> again, when I found and killed the gvim zombie. I get quite different
> answers from different tools as well :
> 
> df tells me I've used 36 Gbytes, that is, the whole disk.
> Filesystem           1k-blocks      Used Available Use% Mounted on
> /dev/hdb1             38464340  36316120    194316 100% /home
> 
> But when I try to find where it has gone with du,
> 
> du -k /home yields :
> 
>  5708312      .
> 
>  total kb, or 6 Gb. Where is the other 30?
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