OK, so I have figured out one way to make this work myself. Let me tell you how I did it, just in the off chance someone else wants to do this some day...
First I downloaded this hidden start program. This allows you to launch bat files and keep the resulting Command windows hidden:
http://www.ntwind.com/software/utilities/hstart.htmlThen I downloaded this nomousy executable that someone made to temporarily hide the mouse cursor:
http://www.autohotkey.com/forum/topic2197.htmlThen I made a batch file, with the following code in it:
start "nomousy" "C:\Emulators\nomousy.exe" /h
Exit
Then I set my pre and post commands for my Nintendo emulator in Mala to look like the following:
C:\Emulators\hstart.exe /NOCONSOLE "C:\Emulators\nomousy.bat"
There is a screenshot of this attached below.
And it works! Every time I launch a Nintendo game, it runs my batch file, hidden so no cmd windows pop up, and it hides the mouse from view in Nestopia. So you don't see that unsettling mouse cursor when you launch a game.
Then when you exit the game, the script launches again, hidden again, and makes the mouse cursor reappear.
I did this because I didn't want to permanently get rid of the mouse cursor. I still use it for administrative type stuff. The only time I did see it when I didn't want to, was when opening Nestopia. So I'm very happy its working now!
Loadman, if you still want to look into why the pre and post commands couldn't simply run the exe like normal, please let me know and I'd be happy to help test. My guess is that you'd be able to duplicate the problem on your end however.