Based soley on what you described in your first post (it is not a lot of detail to go on, however), I'm saying it is simply the windows choice of screen setting/mode. It is deciding the wrong thing, like maybe 320x200 4 bit color (for example). I can't see it on your machine with my own eyes, though.
This is a familiar problem with people who demand exact performance from video, like me. I will not dare try and tell people how to directly edit the Registry and force video changes, because one slip, and there is no safety net... you monitor electronics are physically toast... fried.... kaput.... no good.... ruined. I have see people screw that up time and again in real life, and repairs cost about $60 to $140, depending on labor.
So what I am saying is that you should try changing the setting via Control Panel. many times, that will not work (e.g., Windoze will set you machine to a different mode for it's own misguided reasons to complex to explain here).
The best way, in my opinion, is to simply let Power Strip do it for you. Get it, and study it (it will take a while, because it is very very powerful in what it can do, and it can fry your monitor, too, if you override it's settings for your specific hardware.... but it does protect you as long as you don't override).
Powerstrip will make the proper settings to let you run whatever resolution, depth, refresh rate you want. It will do a whole lot more, even adjusting video card memory speed and processor speed (very good if your card is running hot and/or unstable). PS is particularly good for games and 3D shooters. It will let you change settings on the fly (even within the game itself). I'd just use it to force Civ to whatever video mode you want. I cannot tell from what you posted (not enough detail) exactly "why" the mode is set by Civ or Windows, but if your OS won't override it for you, Powerstip can.
Sooo........ do what you wish.
But based on what you've posted, that's what I'd do (PS always runs on my machines, beginning at bootup, from the STARTUP directory).
