|Have you tried running explorer.exe from Task Manager? That is the shell for the GUI which displays the taskbar, desktop icons, etc.|
"I cannot honestly tell you how the notification stopped popping up....I just continued to install the updates, played with some system settings, then rebooted a few times, and presto!"
What system settings did you play with in effort to remedy your non-Genuine Windows Installation message?
Have you tried talking with Microsoft about this, or perhaps the person you bought it from?
Apologies if I don't respond to your reply immediately. I don't check this site daily.