Windows 7 laptop takes 20-25 minutes to shut down, even from Safe Mode

In addition you may need to run SFC /scannow more than once to repair the files. If they don't repair then you may need to run a Repair Install.

Simultaneously you need to finish checking the condition of your HD, both by running another Disk Check as suggested by Noel, followed by the HD maker's extended HD Diagnostic CD scan as suggested by F5ing.

Remember to back up your files first, if necessary from a rescue disk:
Copy & Paste - in Windows Recovery Console
Paragon rescue disk recover data

Sorry, yes, I should have mentioned that my backups are already very good (I had a big data loss in 2007 and learned my lesson). When I open WinDlg it says 'SMART status: Fail' next to the drive, and CrystalDiskInfo says 'Bad', so I'm not trusting this drive for anything.

Edit: I tried Soluto and all I really ended up doing was disabling some unnecessary add-ons in my browser - and then it tells me that it'll undo all the changes when I uninstall Soluto? What a terrible program.

I tried to run the HD diagnostic last night, but couldn't finish it (long story). I have run CHKDSK /F though and am running SFC now, I can run the diagnostic later today.

Edit: SFC finished, same message about corrupt files, I've attached the log. It's smaller this time, that must be good. I'll reboot and run it again.


Here's the outcome of CHKDSK /F:


Log Name: Application
Source: Microsoft-Windows-Wininit
Date: 18/07/2012 04:28:24
Event ID: 1001
Task Category: None
Level: Information
Keywords: Classic
User: N/A
Computer: Rachel
Description:


Checking file system on C:
The type of the file system is NTFS.


A disk check has been scheduled.
Windows will now check the disk.

CHKDSK is verifying files (stage 1 of 3)...
2188032 file records processed.

File verification completed.
1338 large file records processed.

0 bad file records processed.

0 EA records processed.

92 reparse records processed.

CHKDSK is verifying indexes (stage 2 of 3)...
2296684 index entries processed.

Index verification completed.
0 unindexed files scanned.

0 unindexed files recovered.

CHKDSK is verifying security descriptors (stage 3 of 3)...
2188032 file SDs/SIDs processed.

Cleaning up 11 unused index entries from index $SII of file 0x9.
Cleaning up 11 unused index entries from index $SDH of file 0x9.
Cleaning up 11 unused security descriptors.
Security descriptor verification completed.
54327 data files processed.

CHKDSK is verifying Usn Journal...
33719856 USN bytes processed.

Usn Journal verification completed.
CHKDSK discovered free space marked as allocated in the volume bitmap.
Windows has made corrections to the file system.

472922111 KB total disk space.
232430008 KB in 412478 files.
628904 KB in 54328 indexes.
0 KB in bad sectors.
2303487 KB in use by the system.
65536 KB occupied by the log file.
237559712 KB available on disk.

4096 bytes in each allocation unit.
118230527 total allocation units on disk.
59389928 allocation units available on disk.

Internal Info:
00 63 21 00 80 1f 07 00 aa 23 0c 00 00 00 00 00 .c!......#......
52 8e 00 00 5c 00 00 00 00 00 00 00 00 00 00 00 R...\...........
00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 ................

Windows has finished checking your disk.
Please wait while your computer restarts.

Has your shutdown time improved at all?

SFC still seems to want a reboot and re-run

Code:

 
7322: 2012-07-18 11:18:16, Info                  CSI    00000349 [SR] Cannot commit interactively, there are boot critical components being repaired

but I suspect that that will not change with another run.
This report did at least seem to complete properly (I'm not convinced about the last one).

once this run of SFC is complete, and you've posted the log file, please download and run the CheckSUR tool from Description of the System Update Readiness Tool for Windows Vista, for Windows Server 2008, for Windows 7, and for Windows Server 2008 R2
and post the CheckSUR.log CheckSUR.persist.log files when complete.

[edit] - at least this time we can see the summary report for your CHKDSK, and there are no bad sectors reported, so it may simply be the massive corruption you had that was breaking things up - and may evenhave caused the SMART failure

Yes, creeping bad sector count is a bad sign! - it possibly indicates worn bearings, a vibration problem, or dust (or something else).

I would suspect that unless we find the root cause of the current problem, your best bet is going to be a clean install on your new drive (which may be a good idea anyhow, to avoid any chance of 'infection' of software problems from this one). You can slave this drive to the new one until you've retrieved the data, and then junk it.

CheckSUR can take literally hours to run, depending on how much work it has to do - patienceis a virtue :)