In the NVIDIA Control Panel, you can manage your global 3D settings, and you can define settings for individual executable files (games, Photoshop, emulators, etc.). But, you cannot do the same for batch files. JPCSP is a Java-based emulator that runs from a batch file, and it's own anti-aliasing is awful. I've changed the global settings of anti-aliasing to "override the application setting" but I see no change. So, I've come to the conclusion that the control panel does not affect batch files, and only .exe files. Correct me if I'm wrong. So...
The Nvidia control panel places restrictions on certain games that don't allow you to force AA. Download Nvidia Inspector, click the wrench icon, search for the game you want, find the column labelled 'AA behaviour flag' and change it from "Treat 'Override any application setting' as 'Application-controlled" to "None".
In some games its there for a reason, certain games don't display correctly with certain forms of AA. In others its just Nvidia being restrictive for no reason.
EDIT- After reading through your post again I see this may not be what you are after. Though you can still try and add the batch file in the Nvidia Inspector and try it through there.