Not sure what you mean by SH3 Commander continuing to run during the game - do you mean that when you launched the game from Commander and then exited the game, the Commander interface window would still be open just where you left it?
Cuz that's not what it does on my install - if I want to do anything in Commander after exiting the game, I have to reopen the program. I always assumed that it shut itself down after launching the game's .exe file, it certainly shuts the window down by itself when the game loads on my rig. And all the changes that Commander should be making to the game are in there.
This may be a stupid question that doesn't need asking, and please don't take offense if it is
- but when you say you are using Commander to start SH3 - you do mean that you're clicking the check mark in the bottom right corner of the interface, the one that says "Launch SH3!" when you put the mouse cursor over it. Right?