When this happens to me it's usually because I've accidentally
copied files to the root partition before mounting another file
system. i.e. There may be files 'under' one of your mount points
that you cannot see because you've mounted the file system on it.
You should be able to check by rebooting into single user,
unmounting /home, /usr /tmp and /var, and checking that there are
no files in the mount points themselves.
Instead of that just re-mount / in another folder ... i.e.
mkdir /mnt/slash
mount /dev/hda1 /mnt/slash
du -chs /mnt/slash/*
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