Microsoft has written Knowledge Base article Q185773 that describes the symptoms and resolution of the subject problem. I quote the symptom section of the article:
Using Winnt.exe unattended installation from an MS-DOS FAT partition on a drive exceeding 4 GB may cause NTFS corruption. Unattended installation parameters would be specified as follows in the Unattend.txt file: \[Unattended\] OemPreinstall = yes FileSystem = ConvertNTFS ExtendOemPartition = 1 When starting for the first time after the Windows NT installation is complete, NTFS corruption will be identified either by the inability to successfully start because of missing or corrupted files or by the following CHKDSK messages: CHKDSK is verifying indexes... Correcting error in index %I30 for file 100 Correcting error in index %I30 for file 100 Index verification completed. CHKDSK detected minor inconsistencies on the drive. Errors found. CHKDSK cannot continue in read-only mode. If the corruption is severe enough, the computer may stop responding (hang) during the GUI-mode portion of setup or various other error messages may also occur. These error messages vary from computer to computer, but usually concern file corruption or missing files on systems where the files actually do exist. The files are reported as damaged or missing because the indexes for NTFS are not setup properly.