I've already spent a lot of time on this problem and I don't think this is security software-related. All I have is MS Security Essentials and it doesn't tend to cause problems like this. I have disabled it and the firewall in my past attempts to diagnose this in the past year or so of it occurring in any case. I don't have any plug-ins and am using a stock theme. Running the standalone installer while MC is already running and telling it to close MC does work, so not sure what the difference could be.
I don't have an unlimited time to spend with all the possible permutations of what could be going wrong, especially since this type of problem seems completely unique to MC on this system. This is compounded because it's not like I can repeatedly trigger an auto update while I try different things (unless there is a commandline switch that will force a redownload of the latest package?) I've given some pretty specific information about what files are hanging and what allows the update process to progress, so I'm hoping someone will have a pretty good idea of what could prevent MC from shutting down it's own components such as JRService.exe. If not, I will just have to add it to the growing list of problems I experience with MC that are seemingly unsolvable.
I can add one more piece of information to this- After exiting MC and manually closing Media Server from the system tray, the Media Center 18.exe process still appears in Task Manager and is currently using 25% of CPU.