We recently started pulling in security updates specific to SQL server and pushing them out. We ran into an issue with kb2977320 where it caused two of our SQL servers to get stuck in upgrade mode. It was hard to track down particularly because our DBA installed SP3 after they started having issues which wiped out almost all traces of this kb being installed.
On that note… SQL Server 2008 R2 Service Pack 3 is not / will not be included or pulled in via Windows Update / WSUS / SCCM
See here for details.
So if you can’t get it pulled into SCCM/WSUS, its not you, its Microsoft :]