Finally got to the broken pc!
Clicked the General tab, and Clicked Selective Startup
Under Selective Startup checked Load Startup items
Clicked the Services tab, unchecked the Hide all Microsoft Services box, and then all services were enabled
Clicked Apply
Clicked OK, Clicked Restart.
Run sfc /scannow > No intergraty violations were found
Run Malwarebytes 11 malware were found and removedMalwarebytes Anti-Malware 1.75.0.1300
www.malwarebytes.org

Database version: v2013.05.12.02

Windows 7 Service Pack 1 x86 NTFS (Safe Mode/Networking)
Internet Explorer 9.0.8112.16421
Rebecca :: REBECCA-PC [administrator]

12/05/2013 11:48:14
mbam-log-2013-05-12 (11-48-14).txt

Scan type: Full scan (C:\|)
Scan options enabled: Memory | Startup | Registry | File System | Heuristics/Extra | Heuristics/Shuriken | PUP | PUM
Scan options disabled: P2P
Objects scanned: 293823
Time elapsed: 27 minute(s), 8 second(s)

Memory Processes Detected: 0
(No malicious items detected)

Memory Modules Detected: 0
(No malicious items detected)

Registry Keys Detected: 11
HKCR\CLSID\{11111111-1111-1111-1111-110011341191} (PUP.GamePlayLab) -> Quarantined and deleted successfully.
HKCR\TypeLib\{44444444-4444-4444-4444-440044344491} (PUP.GamePlayLab) -> Quarantined and deleted successfully.
HKCR\Interface\{55555555-5555-5555-5555-550055345591} (PUP.GamePlayLab) -> Quarantined and deleted successfully.
HKCR\CrossriderApp0003491.BHO.1 (PUP.GamePlayLab) -> Quarantined and deleted successfully.
HKLM\SOFTWARE\Microsoft\Windows\CurrentVersion\Explorer\Browser Helper Objects\{11111111-1111-1111-1111-110011341191} (PUP.GamePlayLab) -> Quarantined and deleted successfully.
HKCU\SOFTWARE\Microsoft\Windows\CurrentVersion\Ext\Settings\{11111111-1111-1111-1111-110011341191} (PUP.GamePlayLab) -> Quarantined and deleted successfully.
HKCU\SOFTWARE\Microsoft\Windows\CurrentVersion\Ext\Stats\{11111111-1111-1111-1111-110011341191} (PUP.GamePlayLab) -> Quarantined and deleted successfully.
HKLM\SOFTWARE\Microsoft\Internet Explorer\Low Rights\ElevationPolicy\{11111111-1111-1111-1111-110011341191} (PUP.GamePlayLab) -> Quarantined and deleted successfully.
HKLM\SOFTWARE\Microsoft\Windows\CurrentVersion\Ext\PreApproved\{11111111-1111-1111-1111-110011341191} (PUP.GamePlayLab) -> Quarantined and deleted successfully.
HKCR\CrossriderApp0003491.BHO (PUP.GamePlayLab) -> Quarantined and deleted successfully.
HKCU\SOFTWARE\INSTALLEDBROWSEREXTENSIONS\215 APPS (PUP.CrossFire.SA) -> Quarantined and deleted successfully.

Registry Values Detected: 1
HKCU\Software\InstalledBrowserExtensions\215 Apps|3491 (PUP.CrossFire.SA) -> Data: Vid-Saver -> Quarantined and deleted successfully.

Registry Data Items Detected: 0
(No malicious items detected)

Folders Detected: 0
(No malicious items detected)

Files Detected: 1
C:\Program Files\Vid-Saver\Vid-Saver.dll (PUP.GamePlayLab) -> Quarantined and deleted successfully.

(end)

Run Automatic diagnose Windows Update
Run Windows Update Readiness tool
Still Windows hangs on shutting down
Problem persist!! But not in Safe Mode!
Would a Windows 7 repair solve the problem?

Win7 32bit will often display "Waiting to close background programs" on shut down (I often get that if I shut down soon after video editing with Sony Vegas and it only lasts for a few seconds.) It's possible that for some reason that message is not being displayed due to a background process preventing a normal shut down. Might be due to a currupt OS or program file...

I would be inclined to run a HitmanPro scan http://www.surfright.nl/en just to check that Malwarebytes hadn't missed anything.

Run HitmanPro - No Identified threats (Traces 0)

Just lost for solutions to the shutting down problem!

check windows event log (both application and system) for any strange errors at the time the shutdown "hangs".

Are you getting the mouse click options of sleep, restart, shut down, etc. from the GUI? Very infrequently they do fail to appear on my Win7 machine and I have to shut down by pressing the power button for a few seconds. If that does happen though I get a boot message on start up from bios telling me that the OS didn't shut down properly and do I want to start the OS normally. After that things are fine except for trying to diagnose problems with Win7 which can be a nightmare!

Success at long last!
Run Malware byte and Hitman Pro and deleted some malware remnants.
Run Automatic diagnose Windows Update
Run Windows Update Readiness tool
Still Windows hang on shutting down
UPDATES ARE DOWNLOADED (ONE AT A TIME) McAfee reported that computer was at Risk but it wouldn�t let me turn on the Real-Time scanning or update it, when I restart by pressing the power button and start it again the update showed as installed!
After having a good look at the Event Viewer for Windows Applications and System there were some errors related to McAfee! I uninstalled McAfee and an IE toolbar from SweetPacks and HEY PRESSTO I shut down Windows with no problem!
All the functionality from the Start > sleep, restart, shut down, etc. from the GUI do now work! Problem solved!
Installed AVG Free and created a Restore Point.

McAfee strikes again!

I had exactly the same problem and having read all the possible cures read to the bottom and just tried removing my Virus checker (in my case, Avast). Success! The computer will now shut down sucessfully, even after uploading several Windows updates. One of those updates was Microsoft Security Essentials, which claims to do all that other free Virus Checkers do. So perhaps, it was MSE and Avast that were incompatible. For the moment I'm sticking with MSE as my virus checker and Windows Firewall as my firewall. Let's see how that works.

In reply to a post by nicwright:

...So perhaps, it was MSE and Avast that were incompatible. For the moment I'm sticking with MSE as my virus checker and Windows Firewall as my firewall. Let's see how that works.

I always understood that having more than 1 antivirus product running on a PC was a BAD idea and cause assorted unexpected problems.