Chkdsk in Vista 32-bit SP1 is corrupting security descriptors

I have a Intel DG965WH desktop board and yesterday I did a chkdsk /f run ine command which I thought will be a good thing to do. But it actually brought my operating system down and it started giving me error messages about some Major Bug or so in Windows. Also from some folder and files, the Security descriptor information has been removed. Also Chkdsk log file has got some error messages in it which tells use that the two security data stream entries cross page boundaries. I even tried the backup and restore function but it was not able to recognize my Backup drive. I have a Sata, AHCI drive, so Vista is unable to support it. Please help me out someone.

Even I was facing the same issue on my Vista operating system but I had earlier made a complete system backup and there was able to restore its parition by using the Vista DVD with only restore system drive option. But even after the restore when ever I ran chkdsk then I was getting the same error that was making Vista unbootable. So after checking for various solutions, the only option left for me was to freshly install the operating system and its applications.