I work in State government and have a Windows 2008 R2 Server that failed on updates starting March 20, 2012. Until that point, updates were downloading and installing fine. Now it fails with a Code 8000FFFF every time. I have done the following during the course of troubleshooting this issue:
2. Tried installing updates one at a time
3. Disabled anti-virus software
4. Run System Update Readiness Tool
5. Run System File Checker tool (SFC.exe)
6. Reset the content of the Catroot2 folder
7. Tried to remove HKEY_LOCAL_MACHINE\COMPONENTS -> PendingXmlIdentifier, NextQueueEntryIndex, and AdvancedInstallersNeedResolving, but none of them existed on this machine.
8. Registered Windows Update DLL files
9. Renamed the SoftwareDistribution folder
10. Rolled back all updates installed since the server went into production status
None of the above items has resolved the issue, updates will still not install. As a note, we are running several servers with the exact same build and have not encountered this issue.