Two issues I've noticed and have been able to consistently reproduce...
1) If you load a saved game (SP for sure, possibly MP), exit that game to go to the main menu, then try and start a new game, you cannot access the game options or victory options once you've selected a map...
2) If you hit your hotkey to turn the game into window mode, then exit the game, the next time you start the game it will start in window mode...okay, that seems logical, no problems there...however, I didn't want the game to be in window mode so I hit my hotkey again to turn it to fullscreen...unfortunately, every time I went back to the main menu, the game spontaneously reverted to window mode, which became rather annoying...had to go to the setting file, change it to fullscreen, then start the game...