I had a similar situation on a Windows 7 laptop where nearly 500 GB was "missing" on my system partition. The partition was full, but Windows Explorer was unable to detect the missing space, and the "windirstat" program simply showed a 500 GB "unknown" entry.

However, the TreeSize Free (Administrator) program (TreeSize Free - Quickly Scan Directory Sizes and Find Space Hogs) was able to show what the problem was, namely that someone had misconfigured the Cobian Backup program such that the source and destination directories were the same. As a consequence, it recursed until the partition filled up AND made nearly infinitely long directory paths that neither Windows Explorer nor windirstat were able to handle.

Perhaps needless to say, none of the Windows directory removal tools, including cmd rmdir, would work to remove this mess and it was with great difficulty that I finally managed to clean it up.