Military CAC access no longer works after OS 10.13.2 upgrade

I use an external Common Access Card reader to access secure websites for work. This CAC has ID certificates loaded onto it for security purposes and allows access to secure sites. There are different certificates for different sites.

Prior to macOS v10.13.2 it worked flawlessly. Right after upgrading I attempted to use Safari like I normally do, and while I was banging away on buttons, a window popped up asking me something. In my haste, I just clicked clicked yes, and there starts my issue.

I immediately realized that I had never seen that message before. Even the window it was in was a different gold color than I've seen before. I don't know exactly what it asked me, but I'm assuming that it was asking something about using one of those certificates as a default for accessing sites as a feature new to 10.13.2 as opposed to the previous version where I would have to choose from a list of certificates each time I attempted to access a site.

Now, each time I try to access one of those sites, I get a window that says

<com.apple.webkit.networking is attempting to authenticate the user>

and asks for a passcode. Regardless of what I enter for the password, after pressing Enter, the window disappears and then reappears shortly thereafter asking the same question. It will do this as many times as I attempt to press Enter, all while not loading the page.

I have tried deleting all of the certs and websites in Keychain and reloading the certs, but nothing changes. I have searched the web and the computer help search box for this com.apple.webkit.networking thing (I don't even know what to call it) but cant find anything helpful.

How can I find the setting within the computer that is defaulting to this one certificate and remove that action so I can go back to choosing the certificate I need?