Adding Bad Clusters to the Bad Clusters File - Second NTFS Boot Sector Is Unwriteable

I was using Windows 7 and, as such, was using hard drives formatted in NTFS and divided into several partitions.  I booted the system with an Acronis True Image Home 11 boot CD, made an image of one partition, and saved it on another.  When I rebooted Windows, the folder that I had told Acronis to create (named "2012-01-20 Backup") did not exist.  Windows Explorer showed it as being just a file, without an extension.

In Windows Explorer, I right-clicked on the drive and selected Properties > Tools > Check now.  I clicked both boxes (i.e., "Automatically fix file system errors" and "Scan for and attempt recovery of bad sectors") and then Start.  But the tool did not run.  It just disappeared.  That was probably because I had a paging file on that drive (Start > Run > SystemPropertiesAdvanced.exe > Advanced tab > Settings > Advanced tab > Virtual memory > Change).  I could have changed that, and then rebooted to make the change effective, and then gone back into Windows and tried again.

Instead, I rebooted with a Windows 7 installation DVD and went into Repair your computer > Use recovery tools > Next > Command Prompt.  At the prompt, I typed C: and then DIR, and then D: and then DIR, and so forth until I found the troubled partition.  I typed CHKDSK /R and let it run.  In stage 2 of 5, it deleted the index entry for the 2012-01-20 Backup folder (which it was calling "file 1045").  So it looked like I was going to have to redo my Acronis backup.  After finishing stage 5 of 5, it said this:

Free space verification is complete.
Adding 602 bad clusters to the Bad Clusters File.
CHKDSK discovered free space marked as allocated in the volume bitmap.
The second NTFS boot sector is unwriteable.
Failed to transfer logged messages to the event log with status 50.

That last message didn't bother me -- I was always getting that when I ran CHKDSK this way.  But I wanted to know more about the others.  This was the second time I'd had this kind of problem after running Acronis.  I wondered whether the problem was with the drive -- that perhaps I should get rid of it -- or whether it was instead something that Acronis was doing to the drive.

What I had done previously was to try to resize the partition using a GParted Live (i.e., bootable) CD -- or, actually, I had booted an Ubuntu Live CD (version 10.10 -- apparently not all versions had GParted built in) and had gone into its System > Administration > GParted option.  If I recalled correctly, GParted had been unable to resize the partition, apparently because of the partition's problems, so my next approach was to remove everything from the partition and then use GParted (or possibly Windows Start > Run > diskmgmt.msc) to delete and recreate it.  That had worked last time, so I decided to do it again.  This was the last partition on the drive, and the consensus seemed to be that the second NTFS boot sector was at the end of the partition.  I had used this Acronis CD for a long time, and had not otherwise been getting this problem.  So I thought this time I would create another small partition, after this one, and just let it sit.  If Acronis was getting confused when it wrote to the last partition on the drive, that little 1.5GB partition might provide a buffer and solve the problem.

So now I was going to try to find out whether it was indeed a hard drive issue.  (One other note:  as I continued in the process, it appeared that the Acronis backup may have come very close to filling the troubled partition.  I wondered whether that could somehow have corrupted it.)

I went into GParted again.  It showed an exclamation mark next to this partition.  When I right-clicked on it and looked at Information, it said several things, including these:

ERROR:  This software has detected that the disk has at least 602 bad sectors. . . . This means physical damage on the disk surface caused by deterioration, manufacturing faults or other reason.  The reliability of the disk may stay stable or degrade fast. . . . Unable to read the contents of this file system!  Because of this some operations may be unavailable.

This number of bad "sectors" matched the number of bad "clusters" reported by CHKDSK (above).  That is, it appeared that there might be no bad sectors other than those that were reported after the Acronis process.  I rebooted into Windows and continued to use the system as usual while moving my data off the troubled partition via Windows Explorer.  Then I rebooted into Ubuntu > GParted and, as just indicated, I created two partitions where there was formerly one.  As before, the first of the two was an NTFS partition.  The new addition was that 1.5GB partition, which I formatted as ext3 (invisible to Windows, thus causing no confusion).  Then I did another Acronis image of my programs drive (C:), as before, saving the image to the new NTFS partition.  When Acronis was done, I went back into Windows and saw that Acronis had created what appeared to be a valid image.

I ran System Information for Windows (SIW) to find out which drive this new partition was on, and who made that drive.  After consulting with Disk Management (Start > Run > diskmgmt.msc) to figure out whether I should be looking at disc 0 or disc 1, I saw that it was a Seagate ST31000520AS.  I went to Seagate's webpage and downloaded SeaTools for Windows.  (I already had a copy, but hadn't used it for a long time, and wasn't sure it was the latest version.)  I installed it and ran its Short Drive Self-Test (Short DST).  It passed.  I ran a S.M.A.R.T. test.  It passed that too.

It did not appear that this drive was failing.  I hibernated and then booted up with Ubuntu > GParted.  Its Information option saw no problems.  Neither did its Check option.  I rebooted with the Windows 7 DVD and ran CHKDSK /r on both of the new partitions (i.e., including the little 1.5GB trailer).  There were no statements of the kind I had gotten on the previous try -- nothing about deleting index entries, bad clusters, or an unwriteable NTFS boot sector.  What I got was, "Windows has checked the file system and found no problems" and "0 KB in bad sectors."  Of course, all of my data (except for the newly re-created Acronis backup) was still on the other drive, so I didn't expect file errors (and CHKDSK ran somewhat more quickly on the nearly empty drive).

It appeared that the previous warnings had been false alarms, triggered by the use of Acronis True Image Home 11 to save an image that nearly filled the last partition on the drive. 

To round out my investigation, I went back through the random webpages that I had opened up while searching for insight.  One post raised the possibility that I might have been able to use ntfsresize to resize the partition instead of removing its data, deleting it, and creating a new one in its place.  Ntfsresize (and ntfstruncate) were apparently Linux utilities, and it looked like using them could be risky.  There was a report that seemed to confirm that GParted would have reported an error again if it had found a bad sector, so getting no error messages in GParted's Information option apparently implied that the bad sectors were gone.  Evidently the repartitioning had reset them.  One webpage raised the question of whether the partition had been marked as a boot partition.  As I recalled from my glance in GParted, it hadn't.

Another thread alerted me to the thought that I should have run CHKDSK /B instead of /R.  To verify that, I went into a command window and typed CHKDSK /?.  It said, "NTFS only:  Re-evaluates bad clusters on the volume (implies /R)."  I wondered whether CHKDSK /B might have been a shorter response to the whole problem.  It also said, "The /I or /C switch reduces the amount of time required to run Chkdsk by skipping certain checks of the volume."  As Microsoft advised, I wouldn't have relied on those switches by themselves; but since I had already run /R, at this point I could have tried CHKDSK /I /C /B.  (Too bad there wasn't an /M option -- I'd have had a missile.)  Apparently some of these options were not available in earlier (pre-Vista) versions of Windows.

I had run a couple of searches and probably could have gone on indefinitely, but by this point it began to seem that I had already encountered most of the main recent lines of tinkering on the question.  One exception:  I had searched for, but never did find, a tool that would give me a visual representation or map of bad clusters on the drive.  I vaguely recalled that Norton had provided something along those lines, back in the DOS ages.  Defragmenters like Smart Defrag would show a nice, colorful map of disk clusters, but at this point I wasn't aware of a Windows 7 defragger (or other tool) that provided a depiction of bad clusters specifically, so I sent IOBit a suggestion to that effect.