Missing 13 GB from HD - nothing accounts for it

I have a G4 Mac Mini running Mac OS X Leopard with a 40 GB internal drive.
The Finder says I have 2.5 GB available.
When I use the command line and manually have it calculate the size of every folder on the root of the drive (using the "du" command), I get this:
2.1M /Volumes/Mini Server/.fseventsd
129M /Volumes/Mini Server/.Spotlight-V100
0B /Volumes/Mini Server/.Trashes
0B /Volumes/Mini Server/.vol
2.2G /Volumes/Mini Server/Applications
7.5M /Volumes/Mini Server/bin
0B /Volumes/Mini Server/cores
2.2G /Volumes/Mini Server/Developer
12G /Volumes/Mini Server/Library
0B /Volumes/Mini Server/Network
323M /Volumes/Mini Server/private
5.2M /Volumes/Mini Server/sbin
4.1G /Volumes/Mini Server/System
1.1G /Volumes/Mini Server/Users
1.4G /Volumes/Mini Server/usr
(I excluded the folders that were symbolic links)
Note that, when you add up the totals, you get 23 GB.
I got the size of every stand-alone file on the root, and none of the six or seven files is greater than 10 MB, so that's not accounting for the 13.5 GB of missing space.
I've run Disk Utility (Verify Disk & Repair Permissions) and nothing's wrong.
I just have 13.5 GB missing. Gone.
And no, it's not just another partition or anything - it's actually missing.
Has anybody else encountered this before? It's really baffling. I can't run system updates until I get the space back because I don't have enough space.

Can you get online to download WhatSize or Omnisweeper? They are only small programs that will give you a graphical view of where your data is.
I am presuming that you have cleared you caches using onyx or similar and then restarted your computer to erase any old swap files which can get quite large.

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