Those games probably use an ancient method of setting up screen resolutions, which isn't multiscreen aware. Thus, they fail when they try to reset to the previous layout on exit.
You could update the games to properly use xrandr, but that won't work for doom3, ut2k4 and other closed source games.
An easy workaround is to create a small bash script that runs the game, then resets the screens using xrandr, like
Or you could run the game in windowed mode instead, in a maximized, borderless window.
xrandr --output DVI-0 --auto --pos 0x0
xrandr --output DVI-1 --auto --right-of DVI-0
Or you could spawn a second X server, effectively sandboxing your game.