I did just run the "auto fix" option in the link above. The tool looked exactly the same as the one you previously suggested. Tried a manual launch to update MS Security Essentials and it still bombs out like before. I did know that MS Security Essentials updates were through Windows Updates because they all show up in the Windows Updates history log too.
Here's the results of this running of Windows Update Fixit:
Issues Found
Service registration is missing or corrupt: Not fixed
Reset service registration: Succeeded
Problems installing recent updates: Not fixed
Repair Windows Update: Succeeded
Problems installing recent updates: Not fixed
Repair Windows Update: Succeeded
Check for missing or corrupt files: Fixed
Repair missing or corrupt files: Succeeded
Windows Update error 0x8007000D(2013-11-13-T-11_39_49P): Fixed
Resetting Windows Update data store: Succeeded
Issues Checked
Windows Update environment variables are incorrect: Checked
Some security settings are missing or have been changed: Checked
Windows Update services are not running: Checked
Cryptographic service components are not registered: Checked