Dirty Drive/unable to defrag disk..problem with autochk.exe

I have been unable to run Backup and Restore as well as Defrag from Control Panel. I ran sfc /scannow and checked the cbs.log for curropt files. 3 files were identified as corrupt and unable to be repaired: autochk.exe, tcpmon.ini, and settings.ini. The recovery drive (d is also corrupt but I have the install DVD.
Below is an excerpt from the log:

2014-02-09 19:36:21, Info CSI 0000023c [SR] Verify complete
2014-02-09 19:36:21, Info CSI 0000023d [SR] Repairing 3 components
2014-02-09 19:36:21, Info CSI 0000023e [SR] Beginning Verify and Repair transaction
2014-02-09 19:36:21, Info CSI 0000023f Hashes for file member \SystemRoot\WinSxS\x86_microsoft-windows-autochk_31bf3856ad364e35_6.0.6002.18005_none_e3df6655bee2ee3b\autochk.exe do not match actual file [l:22{11}]"autochk.exe" :
Found: {l:32 b:IsDZ1piuHQPJe74V80McYpCbgG9LjR04JToDujtcps0=} Expected: {l:32 b:u1EGWTHmHtvJIJJNlrUC1G4pZ/+vzliRcfwNOtQ0Y8s=}
2014-02-09 19:36:21, Info CSI 00000240 [SR] Cannot repair member file [l:22{11}]"autochk.exe" of Microsoft-Windows-Autochk, Version = 6.0.6002.18005, pA = PROCESSOR_ARCHITECTURE_INTEL (0), Culture neutral, VersionScope = 1 nonSxS, PublicKeyToken = {l:8 b:31bf3856ad364e35}, Type neutral, TypeName neutral, PublicKey neutral in the store, hash mismatch
2014-02-09 19:36:21, Info CSI 00000241 Hashes for file member \SystemRoot\WinSxS\x86_microsoft-windows-p..rtmonitor-tcpmonini_31bf3856ad364e35_6.0.6001.18000_none_d278d2aaa749970e\tcpmon.ini do not match actual file [l:20{10}]"tcpmon.ini" :
Found: {l:32 b:as3OOcx5px0XiJa7f7s9BVvlW/FFlKR4NMU/T+UP/Kg=} Expected: {l:32 b:ENtKeUct91LKlHclgfWTvnCdCOHHwDe+SYrPzZTTezU=}
2014-02-09 19:36:21, Info CSI 00000242 [SR] Cannot repair member file [l:20{10}]"tcpmon.ini" of Microsoft-Windows-Printing-StandardPortMonitor-TCPMonINI, Version = 6.0.6001.18000, pA = PROCESSOR_ARCHITECTURE_INTEL (0), Culture neutral, VersionScope = 1 nonSxS, PublicKeyToken = {l:8 b:31bf3856ad364e35}, Type neutral, TypeName neutral, PublicKey neutral in the store, hash mismatch

2014-02-09 19:36:21, Info CSI 00000243 Hashes for file member \SystemRoot\WinSxS\x86_microsoft-windows-sidebar_31bf3856ad364e35_6.0.6002.18005_none_d0c824c923c9e622\settings.ini do not match actual file [l:24{12}]"settings.ini" :
Found: {l:32 b:ntPb8a3owMmbzl2TXFHogrOTUqnXgzASIdBVmJptaGE=} Expected: {l:32 b:v6OQf2AJO5FVbRBJuIwXxkdkCoOaSk3y0ol6uTH491o=}
2014-02-09 19:36:21, Info CSI 00000244 [SR] Cannot repair member file [l:24{12}]"settings.ini" of Microsoft-Windows-Sidebar, Version = 6.0.6002.18005, pA = PROCESSOR_ARCHITECTURE_INTEL (0), Culture neutral, VersionScope = 1 nonSxS, PublicKeyToken = {l:8 b:31bf3856ad364e35}, Type neutral, TypeName neutral, PublicKey neutral in the store, hash mismatch

2014-02-09 19:36:21, Info CSI 0000024b Hashes for file member \SystemRoot\WinSxS\x86_microsoft-windows-sidebar_31bf3856ad364e35_6.0.6002.18005_none_d0c824c923c9e622\settings.ini do not match actual file [l:24{12}]"settings.ini" :
Found: {l:32 b:ntPb8a3owMmbzl2TXFHogrOTUqnXgzASIdBVmJptaGE=} Expected: {l:32 b:v6OQf2AJO5FVbRBJuIwXxkdkCoOaSk3y0ol6uTH491o=}
2014-02-09 19:36:21, Info CSI 0000024c [SR] Cannot repair member file [l:24{12}]"settings.ini" of Microsoft-Windows-Sidebar, Version = 6.0.6002.18005, pA = PROCESSOR_ARCHITECTURE_INTEL (0), Culture neutral, VersionScope = 1 nonSxS, PublicKeyToken = {l:8 b:31bf3856ad364e35}, Type neutral, TypeName neutral, PublicKey neutral in the store, hash mismatch


I seem to have resolved the issue with tcpmon.ini and settings.ini files, however, the autochk.exe persists. I could use some help figuring out what to do.

I replaced autochk.exe in c:\windows\system32 with the good file from the install dvd manually but the drive is still corrupt and the log still reports 'hash for file member...do not match actual file' remain. I looked in the directory c:\windows\winsxs and noticed there are multiple directories containing the autochk.exe file, BUT there is only one of them on the install dvd. I believe this is where the fault lies.

The directory on the install DVD contains '18000' in the directory name. A directory of the same name also exists on c:\windows\winsxs BUT there are additional directories on my c: drive (for example, one contains '18005' in place of '18000'..). All of these files begin 'x86_microsoft-windows-autochk..'.

There are also a ton of additional directories all associated with these 'extra' autochk.exe files that exists on my c: drive. They all have '18005' in the directory name for example rather than '18000'.
Here's one of the 'extra' directories: C:\Windows\winsxs\x86_microsoft-windows-autofmt_31bf3856ad364e35_6.0.6002.18005_none_e7dfb5e9bc4fe324.
C:\Windows\winsxs\x86_microsoft-windows-autofmt_31bf3856ad364e35_6.0.6001.18000_none_e5f43cddbf2e17d8 is just below it and also on the install DVD.

Should I remove these extra directories and their associated files? Is there a efficient way to do so that allows me to retain my personal files and programs (ie, I don't want to reinstall Vista and I prefer not to remove the directories one by one).

I appreciate your input.

[DEL]Do you have one here:

"C:\Windows\WinSxS\x86_microsoft-windows-autochk_31bf3856ad364e35_6.2.9200.20717_none_df774bf9ac0a075d\autochk.exe"

That is the one with the most rexcent date that I have in winSXS on my Win 8 Pro X64 system.[/DEL]

Sorry, forgot this is a Vista forum. Let me see what I have foir Vista. Will post back in a bit.

Does your installation disc have the repair option? If so, you should backup your personal files to disc or another drive and run the repair.

I think this might help here. You could try forcing the system to "un-dirty" the drive which may at least allow you to proceed with something else.
You have to do it in en Elevated Command Prompt
Click the Start button and type cmd into the Search box and when cmd or cmd.exe appears in the list above right-click it and select Run as Administrator.

In the window type fsutil dirty query C: and hit Enter (substitute another drive letter if necessary)
From what you typed above it should come back and say it is dirty
Now you can remove that label by typing the following in and then hitting Enter
chkntfs /x C: (with those spaces and change the drive letter if necessary).

I suggest backing up your stuff now. Perhaps this will help: Chkdsk.exe or Autochk.exe starts when you try to shut down or restart your computer