Are you hitting "E" to apply the change? Some graphics changes need to be applied, which means a loading screen.
try /reloadui or try quitting the game completely after changing the setting.
look up the running processes on your computer when you have the game going. It'll be easy to spot. search for that process name in your installation folder and give that permissions. But I'm doubting it's permissions causing your issues.
also check that the setting under resolution is set appropriately. If you choose 1920 x 1200 but have it set to display quality like it's at 800x600 it's going to look bad.