We have released a fix for the synchronization issues that Cecilia described in http://blogs.technet.com/wsus/archive/2008/06/18/client-server-synchronization-issues.aspx. For details on how to obtain the update, please refer to http://support.microsoft.com/kb/954960.
If you are installing the update on Server 2008, you need to install the update with elevated privileges or else install will fail. E.g., you can run it from a command prompt that was launched with "Run as administrator”.
We have now addressed this matter by replacing the original cab'ed MSP with a an exe-wrapped version of the original MSP to avoid this extra step.
The update does not support uninstall or have an entry in Add/Remove Programs. But one can verify the update has been installed by checking that the version of Microsoft.UpdateServices.WebServices.Client.Dll (in %Program Files%\Update Services\WebServices\ClientWebService\bin\) is 3.1.6001.66 (it will be 65 if the update has not been applied).
While this update is only available on Download Center today, we are working on making it available through the WU/WSUS pipeline and hope to have that done as soon as possible.
WSUS Lead Program Manager