250G Disk space has filled up, but DiskInventory only adds up to 60Gs?
Hover your mouse over the large grey box and below it will show the path to that file.  Most likely it is your local TimeMachine backup data.

OS X will keep TimeMachine backups local to your system so that you can do faster restores or if your main TimeMachine system is not available.

From the Apple Menu, select System Info and then click the Storage tab.  You will see how much space "Backups" are using on your disk.

This space will be automatically cleared as you need more disk space.  It is not really considered used space from the user's perspective.  If you Get Info on your drive, the Used Space value will not include it.

For more details on this feature, see this Apple Support Document HT204015

If it isn't TM data or it is some other unnecessary cache file, and it is a file that you are sure you want to remove, right click on the grey box and select "Move to Trash".

And if you don't want local TimeMachine backups at all, open Terminal and type sudo tmutil disable.  If you need to re-enable them, type sudo tmutil enable



FOLLOWUP 2016-04-19:

The large grey box is "Space occupied by other files and folders" because you have the "Show Other Files" option enabled in the Preferences.  Those are system files that you don't have access to read, and/or files outside of the scanned folder. It appears you started at the top of the drive but it can't access the files/folders not owned by you (i.e. root).  You can see in the picture of the .Spotlight-V100 folder it has a red hyphen icon meaning you don't have access.

Since you can't [easily] run the app as root, here is another option but it will take more work.

Open the Terminal app and type the commands cd / then sudo du -hxs .[^.]* *. This will show the size of each directory tree. For example,

 68M    .DocumentRevisions-V100
  0B    .PKInstallSandboxManager
2.0G    .Spotlight-V100
  0B    .Trashes
  0B    .dbfseventsd
  0B    .file
 44M    .fseventsd
  0B    .vol
 21G    Applications
7.0G    Library
  0B    Network
8.2G    System
292G    Users
4.0K    Volumes
2.5M    bin
  0B    cores
4.5K    dev
4.0K    etc
  0B    home
  0B    net
5.4G    private
1.0M    sbin
4.0K    tmp
1.4G    usr
4.0K    var


You can then cd into each large dir and list the files with ls -alh or repeat the sudo command until you find the large files.

Do NOT delete any files unless you know exactly what you are doing.  All of the files/folders outside of the Users folder are for the system.  If you remove the wrong one, you will have a bad week!