I spent a lot more time debugging over the weekend and I think I might have the problem under control for now. I think this issue might really be be an issue with my PC rather than Plex.
My suspicions were that the issue might have been either with windows or with my C drive. Previously I did my windows windows reinstalls with the setting that preserves data, but I suspect that maybe that reset was flawed.
I changed my boot drive and did a completely new install of windows to it. Also this time I’m only going to install applications when I need them as opposed to installing all my usual applications in one go, that way if one of them is causing a conflict it will be easier to narrow it down.
