Windows 7 - Missing files after running Startup recovery

Dear Experts,

I purchased a new HDD and installed Windows 8 on it. The computer already was running WIndows 7 on a separate HDD. I would just choose which HDD to boot in BIOS. It was ok at first but a few days later, Windows 7 wouldnt boot and it would kickoff Startup repair which it was unable to fix. I've tried runnig bootrec.exe, kicked off startup repair multiple times etc.  

I removed the Windows 7 HDD and mounted it to my laptop using USB-to-SATA adaptor, I tried to access the data (My Documents, My Pictures etc) but lot of the files are missing.
For example, I can access certain folders and it would have files where another folder in the same level will have nothing in it when it should.

I've already changed the Security permission so Everyone have full access at the top-level folder (C:\users\username).

What got me baffled was as I've mentioned above, some of the files are there and not the other. Eg, In 'My Pictures' folder, photos in January folder will be there but nothing in the February folder. I have not deleted anything and all these files were definitely there when I was able to boot into WIndows 7.

Is it some security settings preventing access to these folders hence the contents are not displayed? Is there some tool that allow me to view the entire contents of my HDD regardless of security settings?

Thank you.
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JohnBusiness Consultant (Owner)Commented:
I've tried running bootrec.exe, kicked off startup repair multiple times etc.

I wonder if this action may have damaged the users folder. The files would not self-destruct and mounting the disk in a carrier to put in another computer would not delete files either.

From the other computer, are you able to manage permissions to the subject folder and re-apply "Everyone" to it?

.... Thinkpads_User
alexkimAuthor Commented:
Hi thinkpads_user,
Thanks for your reply. Yes - I've already tried that but no difference..
I'm currently running a chkdsk, lots of 'deleting index entry' and 'recovering orphaned file' showing.. its gonna take a loooong time to finish..
JohnBusiness Consultant (Owner)Commented:
Chkdsk does not usually do a good job of recovering orphaned files, at least in my experience. See what happens. You may be more fortunate.

... Thinkpads_User
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alexkimAuthor Commented:
*Fingers crossed*  - any other tool you could recommend?
JohnBusiness Consultant (Owner)Commented:
You could try "recuva". This tool can recover deleted files, but I have not used it.

... Thinkpads_User
Emmanuel AdebayoGlobal Windows Infrastructure Engineer - ConsultantCommented:
Recuva is very good to recover. Please just ensure that you are not written to the hard disk until you perform the recovery.

David Johnson, CD, MVPOwnerCommented:
take ownership of the c:\users directory
from an elevated command prompt
takeown /f c:\users /r /d n

Open in new window

one simple thing ,Please check your folder are hidden or not.
you can recover the files using recovery tool, but some file you will not get proper form.
here is how i handle bad disk drives :

here some links for recovery software :      pc Inspector -FREE -            FREE  -  Recuva                              Stellar                              GetDataBack                              Ontrack                              RecoverMyFiles

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JohnBusiness Consultant (Owner)Commented:
@alexkim  - Please update us after chkdsk has finished. It is possible the files are gone. Multiple repairs will overwrite the disk making it hard or impossible to recover all the files.

.... Thinkpads_User
i only run chkdsk -AFTER a diag states the disk is OK
otherwise, it only creates more problems..
alexkimAuthor Commented:
Thanks guys for your comments - much appreciated!
@ve3ofa and sanjayrajt, I've already done what you guys have suggested prior to chkdsk.. unfortunately that didnt fix the problem..

Now the frustrating part, I kicked off the chkdsk process while I was at work, I left it going overnight and when I got to work this morning, the USB-to-SATA adaptor is not working.. although chkdsk did finish.. below is the trimmed result:

Deleting index entry Trash_CentralPipeStation_LOC_ESN.upk in index $I30 of file 381705.
Deleting index entry SCF952~1.PNG in index $I30 of file 381840.
Deleting index entry fr.lproj in index $I30 of file 391058.
Deleting index entry PL7D4D~1.LPR in index $I30 of file 391058.
Deleting index entry PL7D4D~1.LPR in index $I30 of file 391302.
Deleting index entry localshapes.rcc in index $I30 of file 393257.
  551472 index entries processed.
Index verification completed.
CHKDSK is scanning unindexed files for reconnect to their original directory.
  10693 unindexed files scanned.
12 percent complete. (11495 of 10693 unindexed files scanned)
Recovering orphaned file FinancialDistrict (307736) into directory file 307734.
14 percent complete. (425935 of 430064 files processed)
Windows replaced bad clusters in file 427816
of name \PROGRA~3\MICROS~1\Windows\WER\REPORT~1\NO2B90~1\Report.wer.
  430064 files processed.
File data verification completed.
CHKDSK is verifying free space (stage 5 of 5)...
  52983645 free clusters processed.
Free space verification is complete.
Correcting errors in the master file table's (MFT) BITMAP attribute.
Correcting errors in the Volume Bitmap.
Windows has made corrections to the file system.

976657407 KB total disk space.
763910676 KB in 363290 files.
278404 KB in 60700 indexes.
0 KB in bad sectors.
533747 KB in use by the system.
65536 KB occupied by the log file.
211934580 KB available on disk.

4096 bytes in each allocation unit.
244164351 total allocation units on disk.
52983645 allocation units available on disk.

I guess I gotta wait till I get home to mount the disk to the original PC to see how the chkdsk performed..
it can be necessary to run it again..or requires a couple of restarts
but if possible, do not run it over usb..
alexkimAuthor Commented:
Sorry for the delay in my reply..

Chkdsk sort of worked.. all my missing files are in found.000 and found.001 folders so it seems. I made myself the owner of the foldrers and gave full control access to 'Everyone' user.

Now I just gotta sort through 16000+ xxx.chk folders and find the files I need.. *sigh*
you'll have something to do the next couple of days, i fear
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