DiskInventor & OmniDiskSweeper shows different size as Disk Utility
The biggest issue here is that you need to run your analysis tools as root. If you don't do this, you'll only see the files that your account has access to, and so you won't see everything that is taking up space.

I like GrandPerspective personally. If it's in your Applications folder, the command to run it as root looks like this:

sudo /Applications/GrandPerspective.app/Contents/MacOS/GrandPerspective