Can't see the image, but i think i can help. Look for these lines
@command_window.x = 320 - @command_window.width / 2
@command_window.y = 288
They're in scene_title. Just change the 320 and 288 to whatever, and that'll move the "new game"etc message box. You'll need to experiment a little, but if you want it to the lower right of the screen, chang the 320 to 530, and the 288 to 320(sorry, can't finsd a screen:-/ )