Hi JL3008:
Something's definitely wrong if you're getting a "not applicable" warning with KB3203621 (Cumulative Security Update for Internet Explorer 9 : December 13, 2016). The documentation in the Microsoft Update Catalog shows that
KB3203621 replaces (supersedes) KB3139929 (Cumulative Security Update for Internet Explorer 9 : March 8, 2016) in the supersedence chain for IE9, and there are no newer updates for IE9 that replace KB3203621, so supersedence can't
be the only cause of these repeated warnings.

It is probably is worth repeating that Vista SP2 users who experience the "Checking for updates..." hangs and slow Windows Updates described in m#l's thread
Updates not working, it has been searching for updates for hours
do not see an error message while the Windows Update Agent is searching the update catalog update catalog (wsusscn2.cab). These "Checking for updates..." hangs occur because Windows Update components for Vista SP2 are
outdated, and not corrupted. Dalai has posted background information at
http://wu.krelay.de/en/info.htm, and two main factors contributing to these "Checking for updates..." hangs" (aside from hardware specs such as 32-bit vs. 64-bit architecture,
CPU speed and amount of RAM) are:
- The Windows Update Agent v7.6.7600.256 (C:\Windows\system32\wuaueng.dll) for Vista SP2 has not been updated since
June 2012 and is not optimized for computers with slower CPUs and limited amounts of RAM
- Microsoft has stopped performing regular purges of ex pired updates for Vista SP2 since Win 10 was officially released on 29-Jul-2015
The error code 8000FFFF you see on your own machine when you run a manual Windows Update, as well as the unexpected "not applicable" warnings you see when you try to install any standalone .msu installer, point to a more serious
problem. According to the AskLeo article What is Error 8000FFFF when I try to install a Windows Vista Update?
and TaurArian's article at http://taurarian.mvps.org/WU_Vista/8000ffff.htm, error code 8000FFFF is simply a
generic error that means "Unexpected Error". Causes can range from a hardware incompatibility for a single update to a corrupted Windows Update Agent or a more serious problem with corrupted read/write/edit/delete permissions for your C:\Windows\SoftwareDistribution
or C:\Windows\System32\Catroot2 folders and/or Windows registry entries.
The free version of Speccy is a "quick and dirty" diagnostic that only gives a snapshot of your important hardware and software components, but if your Speccy profile is displaying incorrect information about version numbers for some of your
recently installed software (e.g., Java, NVIDIA, etc.) it makes me wonder if you have a more serious issue with your system files that go beyond Windows updates.
I re-read some of your earlier posts in m#l's thread, and this issue with the "not applicable" warnings for all your .msu installers dates back to at least October 2016. Is this around the time that you tried re-creating your C:\Windows\SoftwareDistribution
folder, and have you tried running any built-in Windows diagnostics like Check Disk (chkdsk) and System File Checker (sfc)?
32-bit Vista Home Premium SP2 * Firefox v51.0.1 * NIS v22.8.1.14 * Speccy 1.30.728
HP Pavilion dv6835ca, Intel Core2Duo T5550 @ 1.83 GHz, 3 GB RAM, NVIDIA GeForce 8400M GS