I recently provisioned some new servers at a client site, these were the first Windows 2008 R2 servers and because of this WSUS did not have any updates downloaded for them.
As I mistakenly forgot to install relevant Windows Updates before I joined the computers to the domain I then had trouble trying to update the servers because Windows stated that:
Windows Update cannot currently check for updates, because updates on this computer are currently controlled by your system administrator
In order to bypass this I temporarily disabled my Server WSUS group policy and this removed the registry settings specifying my update targets etc… (for more information on these registry settings and using GPO for configuring WSUS clients please see Microsoft KB328010)
However I was still unable to run manual updates, after some more rummaging I found the following key
HKCUSoftwareMicrosoftWindowsCurrentVersionPoliciesExplorerNoWindowsUpdate
When I set the above Dword to 0 I could then run manual updates on the server
Update – 24/07/2012
I came across this problem again the other day and did a bit more digging, the above reg key is controlled by the following setting in Group Policy
Disable and remove links to Windows Update
(User ConfigurationAdministrativeTemplatesStart Menu & Taskbar)
This information was found on Technet – Group Policy Registry Reference
SYS-Admin 
Hats off to the gentleman who has posted, I struggled googling and trying lots of options since 10 days. this fixed my issues. THanks a lot.
-Suresh
By: Suresh Balabrahman on June 15, 2012
at 08:37
Thank you so very much, I was going insane trying to run updates on a server after changing GPO applied…changed this reg key and bingo!!!
AWESOME SAUCE!!!
By: Heath Durrett on August 27, 2012
at 20:09
thanks, this seems like a really bad design.
i thought it was supposed to just remove and disable the links, not the whole thing
By: r2d2 on November 16, 2012
at 10:31
Finally! Thanks a bunch, mate. Funny that even GPO editor does not mention about this nifty little ‘feature’ that comes with this cosmetic change.
By: Mikko on March 14, 2013
at 11:43
Disable – Turn off access to all Windows Update features
under Machine System Internet Communication settings
Pgt
By: Pgt on March 17, 2013
at 16:57
Reblogged this on Nealo's Blog.
By: Nealo on February 21, 2014
at 14:03
Great article. Mainly because I wrote it!
If you’re going to lift a blog word for word.. Then give credit!
😦
By: Nealo on May 11, 2014
at 14:59
Erm please delete my last comment. I don’t seem to have the option to.
Sorry. Tired! :-s
By: Nealo on May 11, 2014
at 15:03