Is it expected to be open in the background?
For your information, if the launcher is already running and I accidentally try to start it again, I get a new config window. Clicking ok gets me an error message and a choice: Carry on with two programs, or quit both. In effect, if you choose to run both, they quit with another error message.
Perhaps you could intercept the first error message and instead print something like "There is already one instance of the application running on your computer"?
edit: And when I try to run a game from the launcher, the title bar includes "THIS IS A COPY" and I cannot open my system view from the Empires drop-down on the main menu bar, as the "system maps" option is greyed out. Also greyed out is the Battle Control window, the Galactic Map, the Task Force window and "update sys control" along with several commands in the "SM" and the "Game" dropdowns.