I run Windows Update manually, and I keep the BITS and "Automatic Updates" services disabled since I discovered years ago that Microsoft was applying updates to my system even though I had told it "Notify me but don't automatically download or install them". However, before running WSA, I enabled BITS and the AU service. Even so, Webroot's "complete report" says:
Auto Update State Disabled
Update Type Auto-Updates Disabled
Last Update Check Never
Last Update Download Never
Last Update Install Never (90 days ago)
Next Scheduled Update Check 2009-06-11 01:29:29
Next Scheduled Install Time Never
but in fact I ran W.U. earlier today and rebooted prior to running this WSA test. The only "updates" W.U. reports that I'm missing are two hidden "High-priority updates" that are not security related.
The update to .NET Framework 3.5 Service Pack 1 for the .NET Framework Assistant 1.0 for Firefox addresses several compatibility issues with version 1.0 of the extension. Details...
The Windows Genuine Advantage Notification tool notifies you if your copy of Windows is not genuine. If your system is found to be non-genuine, the tool will help you obtain a licensed copy of Windows. Details...
See Annoyances.org - Remove the Microsoft .NET Framework Assistant (ClickOnce) Firefox Extension
This update adds to Firefox one of the most dangerous vulnerabilities present in all versions of Internet Explorer: the ability for websites to easily and quietly install software on your PC. Since this design flaw is one of the reasons you may've originally chosen to abandon IE in favor of a safer browser like Firefox, you may wish to remove this extension with all due haste.
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 See Get all security patches without WGA nightmares
Best answer by Kit
If we are able to determine it is a bug, it will be fixed.
If it is a missing feature that would be of benefit to the majority of the users, it may be added.
If it is an environmental issue, you will need to fix your computer in such a way to allow it to work.
Until then you may use it as it is and watch for updates, or not use it as you see fit. It's a free utility.