Every time I restart Splinter Cell: Conviction the mouse is uninverted, forcing me to open the settings menu and enable y axis inversion. This is incredibly annoying. Can I get the game to remember that I've inverted the mouse?
You might just try a small piece of 3rd party software that inverts the mouse all the time, like this guy did. A bootstrap, but possibly less frustrating than fixing it every time.
You are not the only person with this problem. Others have tried manual modification of the .ini agent86 suggests without luck, but as he suggests you may have better success by modifying settings in game when running in admin mode.