Grab
TinkerTool or
Onyx and use one to make all files visible in the Finder.
Once you have the Finder set to show all files, check these locations for large abandoned files:
/VolumeName/Temporary Items/ (used by OS9)
/VolumeName/private/tmp/ (used by QuickTime & SoftwareUpdate)
/VolumeName/private/var/tmp/ (used by the system)
Be careful with
/private/var/temp, this folder contains mount points and other important things that must not be deleted. Only delete large stray files, do not delete folders or any file less than 10 MB. When looking over
/private/tmp, be sure to follow subfolders. QuickTime in particular likes to hide trailer downloads there in invisible subfolders.
If that doesn't do it, hit the logfile folders to see if a runaway logfile has grown huge:
/VolumeName/Library/Logs/
/YourHomeFolder/Library/Logs/
/OtherHomeFolders/Library/Logs/
/VolumeName/private/var/log/
Since your test indicated it is not in the regular visible folders, that most likely means the problem file(s) is/are in
/private/tmp or
/Temporary Items.