Windows Update in Vista SP2 Has Viruses

I have just concluded upgrading my Comodo Internet Security from 3.xxxx and ran Windows Update.
This specific update: Security Update for Windows Media Encoder 9 Series for Windows Vista (KB979332)
is identified by Comodo 4.1.150349.920 DB5088 as Packed.Win32.Klone~AP@107254933 and is prevented from running as part of Windows Update and as a standalone .msi executable downloaded from Microsoft Support.

Have you sent it to comodo as a false positive so it gets fixed?

Yes, please report these as false positives here:
Comodo Malware/False-Positive Submission
and they will be fixed quickly.