So I finally narrowed down the problem for sure this time.
When using IOBit Security 360 the system will randomly become unresponsive.
I finally found proof of this today. I was using my machine one minute and when I went to use it a few minutes later I was not able to do anything at all. The task manager would not open and applications would not launch.
This had been happening over the past week and I originally thought it was due to uTorrent. It turns out it was coincidence alone that I would shut down uTorrent and then the system would have this issue.
So today when it happened I shut down Security 360 and as soon as I did that the system became responsive and ran fine. Simply shutting the app down was enough to solve the issue.
So do not use Security 360 until there is a fix.