See bullet 4 in things I checked in my original post. I did ensure that same account was used to install PMS as well as launch the service(s).
Are you having different user for install from one you run PMS Service under?
If you are, then the auto start would be having in the install account leading to 2 instances.
See my post #4 https://forums.plex.tv/topic/93994-pms-as-a-service/?p=547864
The registry setting is for the user account and would be different depending on which session loads up regedit
