To resolve this I booted off the Vista installation media, and selected repair. It tried to automatically repair startup configuration, and then came back saying it could not. One of the options was to go into advanced repair options. Chose that. Then chose command prompt. At command prompt:
>cd c:
>cd windows
>cd winsxs
>del pending.xml
Once the file was deleted, rebooted system. System went back to installing update 3 of 3 but this time it worked.