Microsoft Knowledge Base Article 303079 contains the following summary:

The NTFS file system supports many volume and file-level features that may lead to what appears to be lost or misreported free disk space . This behavior may be apparent when an NTFS volume suddenly becomes very full for no reason, and yet an administrator cannot find the cause or locate the offending folders and files . This sometimes occurs because of malicious or unauthorized access to an NTFS volume on which very large files or a high quantity of small files are secretly copied, which then have their NTFS permissions removed or restricted . This behavior may also occur after a system malfunction or power outage occurs, causing volume corruption.

This article discusses how to check an NTFS file systems disk space allocation to discover offending files and directories or check for volume corruption. This article is intended for Windows 2000-and-later operating systems that support some advanced storage features and troubleshooting methods; however Windows NT users may also find this article useful. The following is a short list of reasons why the disk space allocation of an NTFS volume may appear to be misreported:
The NTFS volume's cluster size is too large for the average-sized files being stored.
File attributes or NTFS permissions prevent files or folders from being displayed or accessed by Windows Explorer or from a Windows command prompt.
The folder path exceeds 255 characters.
Directories or files contain invalid or reserved file names.
NTFS metafiles (such as the Master File Table) have grown and cannot be de-allocated.
Files or folders contain alternate data streams.
NTFS File system corruption causes free space to be reported as being in use.
Other NTFS features may cause file-allocation confusion.