I think I may be having the same problem with my wife's iMac (no such problem on my MBP, thankfully). The total drive space is 297 GB, the "size of scanned files" is 173 GB (which is what a manual count adds up to using Finder), and Free Space (44 GB) plus "Miscellaneous used space" (80 GB) rounds it out.
The maddening things is that I cannot figure out where this *#$%* 80 GB is hiding!
I have seen comments about running applications as "root" - being a former Windows guy, I've always assumed this just means having local admin rights - but apparently that is not the way it works on a Mac?
Can I (as a local Admin) not see some user's files on this machine? That might explain it, but my wife has ~80 GB in photo files on this machine in her iPhoto library, and I can see THOSE with Grand Perspective, no problem...