I just upgraded our WSUS server from WSUS 2.0 to WSUS 3.0 SP2. After performing the upgrade I ran the Cleanup Wizard. All boxes were checked except for "Computers not contacting the server". It ran for several hours and finally errored out with the Database Error below. At that point I ran the Cleanup Wizard again but only did one option at a time. Superseded Updates, Expired Updates, and Unneeded update Files each run fine and finish in less than a minute. However, if I try to clean Unused updates and update revisions I get the Database Error after about two minutes. I checked the event log after the Database Error and I'm getting event ID 7042 (full details below). The only products I have selected are Office and Windows. My WSUS folder is 27GB and my WsusDatabase folder is 5GB. WSUS seems to be using the Internal Database.
Error: Database Error
An error occurred when trying to perform a database operation. This can happen if the database is very busy, if the database service is topped, or if the connection to the database is lost. Please contact your systems administrator if the problem persists. Click Reset Server Node to try to connect to the server again. "Reset Server Node"
Source: Windows Server Update
Event ID: 7042
The WSUS administration console was unable to connect to the WSUS Server Database.
Verify that SQL server is running on the WSUS Server. If the problem persists, try restarting SQL.
System.Data.SqlClient.SqlException -- Timeout expired. The timeout period elapsed prior to completion of the operation or the server is not responding.
The statement has been terminated.
.Net SqlClient Data Provider
at System.Windows.Forms.Control.MarshaledInvoke(Control caller, Delegate method, Object args, Boolean synchronous)
at System.Windows.Forms.Control.Invoke(Delegate method, Object args)
at System.Windows.Forms.Control.Invoke(Delegate method)
at Microsoft.UpdateServices.UI.SnapIn.Wizards.ServerCleanup.ServerCleanupWizard.OnCleanupComplete(Object sender, PerformCleanupCompletedEventArgs e)
For more information, see Help and Support Center at http://go.microsoft.com/fwlink/events.asp