"Miscellaneous used space: All used space that is not accounted for by the size of the scanned files. This includes the following:
* Files that were not scanned, either because the scanned folder was not at the root of the volume, or the user did not have permissions to access all subfolders.
* Files that are excluded by the filter (if any).
* Disk space that is not accounted for because the Logical file size measure is used, which underestimates the space that files actually take up.
* Low-level file system data, needed to store amongst others the folder hierarchy."
To reduce the size of the miscellaneous used space, you can do the following:
1) Run GrandPerspective as "root" so you have permission to scan all files (see [1])
2) Use the Physical file size measure
3) Scan in the entire HD, without using a filter