You have a good bit of digging you need to do to determine the root cause.
Do you have policies that contain scripts that call System Preferences to open, is that policy running over and over
You can look at a system's LaunchAgents and LaunchDaemons to see if there's a keepalive for system preferences set for whatever reason.
Is your security agents forcing the application open by chance in an attempt to force system updates.
Those are just a few of the possibilities that you could be seeing.
