What causes NTFS index corruption?

I have a relatively new hard disk and it has been working fine all this while. Today, however, on starting Windows a few of my applications failed to load some DLLs. Windows ran chkdsk upon restart and reported a dozen of index issues which it fixed successfully.

After another restart Windows stopped booting altogether and showed a prompt of some missing file.

Now, my question is how did the file index get corrupted out of the blue? Chkdsk showed 0 bad sectors so that shouldn't be the cause of the corruption...

NTFS corruption can be caused by hardware issues like problems with the cable, the controller or a harddrive failing (mechanical problems, ...). If write caching is enabled on the drive, the hardware could not be able to keep up writing the data to disk.

Other common reasons I could think of are system malfunctions (blue screens, buggy RAID controller/drivers) and power outages which could leave the filesystem in an inconsistent state.

Check the Windows event log for the period before the failure. It could contain some useful information what exactly went wrong. And backup your data, if you haven't done it yet. These errors could be the first sign of a complete failure of the harddisk. Run a harddisk diagnostic software to detect if some of the reliability parameters are not ok. You could use the free Active@ Hard Disk Monitor to run some checks.

My guess is that your HD will soon return its magnetic soul.

Run SMART check on the drive and it report errors, get a replacement.