The updates you've listed mainly came from clearos-updates.

Hey Nick, that's what I figured, but I know that ClearOS-Updates was enabled because that's the first one I looked for. Problem is I can't remember which one I had to enable. Wish I had written it down, but I'd swear it was the plain ClearOS repo.

Can you verify if the files in /var/lib/rpm get updated whenever there's an update installed? If you look at the link I shared of an older post, at that time I was getting a repo error in the system log that was dated the same as the files in /var/lib/rpm. I'm not getting one now, but that doesn't mean it's not related.