Having an exe run in bg, unity still responsive

I have an exe that is started by unity, that when it starts sends input to unity that i can use.

I have a problem, that when those exe’s start up , it “freases” unity and you are not able to continue playing your game.

How do i send those console windows to the background and stop it affecting unity at all?

Images attached to what i mean, and my code snipped added below
(the minimize part in my code didnt work by the way… dont know if im doing it wrong…)

Process p;
	// Use this for initialization
	void Start () {
		ProcessStartInfo info = new ProcessStartInfo();
		info.FileName = @"Directory";
		info.WorkingDirectory = @"Directoryalt text";
		info.Arguments = "";
		info.UseShellExecute = false;
		info.RedirectStandardOutput = true;
		//info.WindowStyle = ProcessWindowStyle.Minimized;
		info.WindowStyle = ProcessWindowStyle.Hidden;
		p = Process.Start(info);
		if ( p != null )

You can start your process inside one thread.
See System.Threading