YOu could try to add the .exe of the tool to the exclude list in the vorpX config app. Not sure whether that will help. but it’s worth a shot.
BTW: If you use the tray tool for adding a supersampling multiplier, you should be aware that doing so is not recommended with vorpX since it works different than native apps. The right way to enhance image quality with vorpX is to raise the resolution that you run a game with. Recommended resolutions are 1280×1024, 1600×1200, 1920×1440 depending on what you PC can handle for a game without falling below 45fps.