There are several causes for this:
- The cluster size of the NTFS volume is too large for the average-sized files that are being stored.
- File attributes or NTFS permissions prevent files or folders from being either displayed or accessed when you use either Microsoft Windows Explorer or a Windows command prompt.
- The folder path exceed 255 characters.
- Folders or files contain invalid or reserved file names.
- NTFS metafiles (such as the Master File Table [MFT]) have grown and cannot be unallocated.
- Files or folders contain alternate data streams.
- NTFS corruption causes Windows to report free space as being in use.
- Other NTFS features cause file-allocation confusion.
Microsoft provides various solutions for symptom identified. Reference Microsoft Knowledge Base Articles 315688 (for Windows XP) and 303079 (for Windows 2000) for more information.