Are you running Media Server at Windows login? It will look like MC18 is running if you look at Task Manager.
Take a look at the wiki topic on Media Server for more information.
The service starts after a re-boot as intended and is visible in the tray.
Have you tried using
MC18.exe /close to exit the program? You will no longer be able to find the server icon in the tray and of course will miss any recordings you may have set up
The bug also seems to be present in Standard View, my system is rarely used in any view except theater view hence my earlier reference to it.
I have recorded a log file that I believe captures the issue and sent it to support. Comparing
MC18.exe /close log versus closing with ALT F4 there are an awful lot of Destroy commands being sent ?