This part is a bit puzzling to me. In your setup, which is based on CruelComodo, all unrecognized files should be autocontained. Indeed, you will find that file as a number in the GUI, but the first thing you should see is the program window with a green frame.Unrecognized just when I see a number in the GUI.
So after scratching my head for a minute, I guess you are talking about processes that don't have a visible program window, and/or processes that can't display their program window due to the restrictions of autocontainment. For them, all you will see is a number in the GUI, and you would rather see an alert of some kind.
If I got the story right, you could change the rule for unrecognized files: instead of containing them, block them. Then you should get a Windows error message, and also find a number in the GUI.