Sounds like Opus is already running in the background normally and when you run it again it just tells the existing instance to open a new window.
You can use File > Exit Directory Opus to tell it to quit.
But, outside special situations where there's no alternative, you should generally use the Admin Mode button on the toolbar if you need to do lots of elevated actions and don't want multiple UAC prompts. Launching the whole program elevated instead will break things by making unelevated apps unable to talk to Opus: