Sometimes after cloning a system to a new disk that is Advanced Format it is possible that Windows Update thinks that the update service is not running despite the fact the the service reports to be running in Services.
This is a compatibility issue with Windows and Advanced Format disks.
The following excerpt from Microsoft Support (http://support.microsoft.com/kb/982018) describes the problem in more technical detail:
The Extensible Storage Engine API(ESENT) is a high-performance desktop database engine that is used by many applications, including Windows Update. Certain storage drivers have different kinds of support for querying the physical sector size of the hard disk in a hard disk drive and, when such a driver is upgraded, the reported physical sector size of the hard disk can change. Because of the logging structure of ESENT, applications that are built on ESENT receive an error message and stop responding when the reported physical sector size changes between operating system sessions.
Note Applications that are built on ESENT include Windows Update, Active Directory, Windows Desktop Search, certification authority (CA), WINS, DHCP, and Windows Live Mail.
You receive the following error message when you click the Check for Updates button on Windows Update site:
Windows Update cannot currently check for updates because the service is not running. You may have to restart your computer.
To resolve this issue it is necessary to update storage drivers on your system to detect Advanced Format disks correctly. This will depend on the hardware of your system.
For Intel systems installing the Intel Rapid Storage Technology software often resolves the issue.
There are also some Microsoft provided hotfixes available for this issue depending on your Operating System: