I agree with OldTroll's answer as the most probable cause for your "missing" space.

On Linux you can easily remount the whole root partition (or any other partition for that matter) to another place in you filesystem say /mnt for example, just issue a

mount -o bind / /mnt

then you can do a

du -h /mnt

and see what uses up your space.

Ps: sorry for adding a new answer and not a comment but I needed some formatting for this post to be readable.

I agree with OldTroll's answer as the most probable cause for your "missing" space.

On Linux you can easily remount the whole root partition (or any other partition for that matter) to another place in you filesystem say, /mnt, for example, just issue a

mount -o bind / /mnt

then you can do a

du -h /mnt

and see what is using up your space.