SharePoint users who upgraded from SQL Server 2000 Desktop Engine (WMSDE) to any other edition of SQL Server 2000 (for example, SQL Server 2000 Standard Edition) may be incorrectly offered a WMSDE update for 948110. This problem can occur if the SQL Server 2000 edition is not patched correctly with SQL Server 2000 Service Pack 4 after the upgrade from WMSDE. The WMSDE update may cause SharePoint to stop working. The issue we are discussion does not apply to SBS 2003 R2 users that migrated to SQL 2005 Workgroup Edition.
The symptoms the you will notice is that the service instance (e.g. mssql$Sharepoint) will start and then immediately stop.
In the C:\Program Files\Microsoft SQL Server\MSSQL$Sharepoint\Log\errorlog file you will see the following:
2008-07-09 09:38:33.30 spid2 Skipping startup of clean database id 4
2008-07-09 09:38:33.30 spid2 Skipping startup of clean database id 6
2008-07-09 09:38:33.30 spid2 Starting up database 'STS_Config'.
2008-07-09 09:38:33.38 spid5 Clearing tempdb database.
2008-07-09 09:38:33.41 spid5 Starting up database 'tempdb'.
2008-07-09 09:38:33.44 spid2 Recovery complete.
2008-07-09 09:38:34.35 spid2 Database 'master' has invalid schema. <==Notice the invalid schema.
The Windows Update detection logic is being fixed and this update should not be offered incorrectly to non-qualifying products, this change is still pending and should happen at any time now.
If you are not sure if you have SharePoint was upgraded to SQL 2000, you need to check the ERRORLOG files prior to the update being installed and review the versions reported there. The log files are usually found in C:\Program Files\Microsoft SQL Server\MSSQL$SharePoint\Log\, if you cannot find an ERRORLOG.n file that is older than the time of when the update was installed, try to get an older ERRORLOG from backup or shadow copy.