So, my problem has been resolved by my wonderful neighbor, who discovered that MalwareBytesPro was somehow stuck in a scan mode that was slowing everything else down. To the point where the computer wasn't able to power down completely.
Once he got it to shut down, it was able to reboot, install the updates and open again. At that point, he aborted the MB scan that was in progress and things went back to normal.
This is the second time that MB overloaded the computer. The first instance did show up on Task Manager as excessive CPU useage. This time it did not, but the super slowness was similar.
Now that I know this, I can look at MBAM first and try to unstick it, but I wonder why this has happened twice now. Any ideas? I know I have the switch right to let it interact with Windows Defender so its not that.