Cannot run updates on windows 7

I have this laptop that was brought to me which has multiple viruses & Malware.  After running scans & getting the viruses out of the system, Windows 7 runs fine, gets on the internet fine, but the only problem now is that it will not run updates.  If I select to run updates, it will tell me that it cannot configure updates while system is running and I need to restart the system.  When I restart the system, it attempt to install updates but then it says it cannot install updates and is revertiing.  
What do I need to do to correct this issue?
Will Schmidtowner Asked:
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aadihCommented:
Better do a repair install.
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Thomas GrassiSystems AdministratorCommented:
I would first try to go back to the earliest system restore point.
If recently infected a restore point will be faster.

If truly infected I would get another hard drive and replace it and do a fresh install

What anti virus program you have? If none of the ones listed below then uninstall what is currently on since it is not working properly.  Then follow the procedure below.

Here is a good procedure

Boot up in safe mode with command prompt, and type rstrui.exe to restore to an earlier time.

Download these tools

CCleaner: http://www.filehippo.com/download_ccleaner/
TDSSKiller: http://www.bleepingcomputer.com/download/tdsskiller/
RogueKiller: http://www.bleepingcomputer.com/download/roguekiller/
Adwcleaner: http://www.bleepingcomputer.com/download/adwcleaner/
Malwarebytes: http://www.bleepingcomputer.com/download/malwarebytes-anti-malware/

And run them in that order:

1) CCleaner
2) TDSSKiller
3) RogueKiller (scan, fix host, fix proxy, fix dns)
4) Adwcleaner: (Scan, Clean)
5) Malwarebytes: (download all updates and run a full scan)
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Michael MachieIT SupervisorCommented:
Check the Windows Update settings to make sure they allow all Users to update - it is a check box as seen in the pic below:

Win Update Settings
Perhaps something made a change to the setting.

My next thought it that the Windows Installer package may be corrupt..Try to add or remove any windows feature, like FTP server or something. If it fails or errors out, your Windows Installer package is corrupt.
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Thomas GrassiSystems AdministratorCommented:
It could be failing on one update

Which one is it failing on deselect that one and try the others.

Does this Windows 7 have SP 1 installed?
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Michael MachieIT SupervisorCommented:
Along the lines of what was just suggested by trgrassijr55 perhaps selecting each update file separately will allow you to identify which is failing, if that is the case.

IE/  Start at the top of the list and install the single update and see if it still fails. If not or if so, move to the second and see. If the second updates then the first one is the issue. Etc
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Will Schmidtowner Author Commented:
I ran all the suggested but I am still having the same issue.
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Michael MachieIT SupervisorCommented:
Were you able to add/remove a Windows feature successfully?

If not then your Windows Installer is corrupt..
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Will Schmidtowner Author Commented:
it is not giving me any list of the updates.
Here is what happens:
When I select to run updates, it scans for about a minute and then says: " cannot configure updates while system is running. You need to restart the system in order for windows to finish installing updates."  So, when I restart the computer it restarts and the says that it is configuring windows updates, restarts, comes back on with the same message, only this time it gives a percentage of the update done and when it gets to 100% it says that it is reverting updates, then restarts without attempting updates.

But ... I guess I will have to close this session out because the customer came and picked up her laptop and said she would bring it back later to let me try and get the updates working.
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Michael MachieIT SupervisorCommented:
You can always run a fantastic program called ComboFix that I LIVE by, almost daily.

I am always amazed at what this little utility can do with regards to weirdness that we see in IT every day. It has even resolved issues with updating like you are having. Trust me, try this once on a virus or mal-ware infected machine or on a machine that is acting funky - you will be surprised.

Free, easy to use. Disable any AntiVirus software first and let 'er Rip!

HERE is the link direct download link..
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Thomas GrassiSystems AdministratorCommented:
As I said earlier

you may just need to re install

I would use a new hard drive

never know what virus's she had.
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Will Schmidtowner Author Commented:
Reply to trgrassijr55:
I agree with you and that is what I told the customer when she picked up the laptop.  
Reply to machienet:
I ran ComboFix too after I ran Malwarebytes, then I ran a boot scan with Avast, then the others that trgrassijr55 suggested. I also checked to make sure that all users were allowed to update.
I also went to C:\Windows\softwareDistribution and deleted the contents in all folders (don't know if that was the right thing to do, but I did it anyway).
I downloaded the diagnostic tool from microsoft's website but that didn't help either.
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Michael MachieIT SupervisorCommented:
All i can think of now, aside from a wipe, is to see if you can log in on another profile and see if the issue remains. If so, back up the User's data and delete their profile. Log back in as that User and mobe the data back on.
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Thomas GrassiSystems AdministratorCommented:
Any update?

If the computer truely had a virus then another user profile may not work.
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Will Schmidtowner Author Commented:
I need to close this session out as the customer has picked up her laptop.  She has agreed to brink it back in a couple of weeks and let me wipe the drive and re-install.  I should have done that in the first place, but I wanted to see if there was a way to fix the issue without doing that first.  I did not think about creating another profile, but then the computer was pretty much loaded with viruses. I cleaned out over 200 of them.
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Michael MachieIT SupervisorCommented:
With that many bugs it is best to do a low level format and rebuild like you are going to.
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