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 .NET Framework Assistant is a dangerous addon that Microsoft secretly foisted on Firefox users in 2010 and I don't want it anywhere near my system. The WGA Notification tool is Microsoft spyware that does nothing to improve the security of your system.Update to .NET Framework 3.5 Service Pack 1 for the .NET Framework Assistant 1.0 x86 (KB963707)
Download size: 741 KB , less than 1 minuteWindows Genuine Advantage Notification (KB905474)
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...
Download size: 0 KB , 0 minutes (Downloaded; ready to install)
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
The Microsoft .NET Framework 3.5 Service Pack 1 update, pushed through the Windows Update service to all recent editions of Windows in February 2009, installs the Microsoft .NET Framework Assistant firefox extension without asking your permission.[Redacted]
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.
*Per the Community Guidelines, please do not attempt to promote a separate organization or cause.*
 See Get all security patches without WGA nightmares
If you’re a legitimate Microsoft customer, you can download and install all the Windows updates you need without running Windows Genuine Advantage (WGA) and exposing yourself to the false positives it’s become known for.
Best answer by KitView original
The good news is that it is actually being very accurate.
Your system is missing two updates that Microsoft designates as "Important" or higher. Your choice to hide them and consider them annoying or unimportant is irrelevant to the fact that they are considered important by the operating system and therefore are reported.
It's important to take into account the fact that it will report everything against a global baseline. It's then up to the technician to make an educated decision on the issue. System Analyzer does not install those updates, after all. It doesn't fix the things it alerts. It's not System Fixer. It's a System Analyzer. ;)
So in your case, the proper action would be to say "Okay, it is aware that I do not have these two items, despite the fact that another program I use tries very hard to completely remove those patches from Windows' awareness. Those are two items I don't want to have, so I can safely ignore that alert and consider it to be a baseline for my system."
On the line of Windows Update reporting, I assume that with the preference for PMP, you use it. Being an obviously well-educated user, you likely then know that the program does odd things to the guts of Windows Updates in such a way that causes a permanent change to the system.
Since System Analyzer is baselined against fully-working systems, it's not intended to deal with the changes to the system caused by such things. It will ask Windows for the WU information, and report that. Since that information is broken, it reports the broken information. Again, an intelligent tech just takes that into account for the system baseline.
So, you are correct. While it works just fine on millions of other systems, systems with very off-kilter configurations or specialty systems will get some odd results at times. It just means you've changed and adjusted your system well enough that Windows doesn't know what's going on anymore and so he information it gives to System Analyzer won't necessarily be correct. The smart tech takes this into account and all is good.
If all else fails, take joy in the fact that you've taken control of your system well enough to make the changes in the way you like. But you know your own system best, and no program can ever change that.
As a minor note on the .NET Firefox extension... Firefox itself declared that extension evil and wiped it out a long time ago. There is no good reason to not install the Microsoft patch because it does fix a few other things and it will also allow patches that rely on some of the shared code to operate more efficiently. Unless of course you're working with a very old version of Firefox. In which case, you should update that.
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.