Well, I looked in the conquests.ini file for "keepres," as Commander Bello suggested I add "keepres=1," but there is no such variable, so I'm not sure if the game would recognize it. In any case, it got me to thinking. I checked the ini files for CIV III and PTW, and found that there is a variable which seemed to indicate a refresh rate. It's called, obviously enough, "refresh." On my PTW and CIV III ini files, the line is "refresh=60" - So, if you're having a graphics problem like mine, that is if the monitor appears to be set to the wrong refresh rate when you play the game (the graphics will overlap to the point where you cannot recognize what's going on, sort of like a stereoscopic image without the special lens), then add this line to your conquests.ini file:
refresh=[refresh rate of your monitor at the resolution you play the game]
Make sure to put it on a line by itself - don't add this value to the end of another line. In my file it looks like this:
[Conquests]
Voice Quality=0
refresh=60
Prefs Format=1
.... (more values - do not add dots or periods like that, just here to show there are more below "Prefs Format=1")
... because that's about where it was in the CIV III and PTW ini files. I don't think it matters where you put it, as it usually doesn't matter in ini files, as long as it's on its own line like the others.
So, there ya go! Am going to add this to the bugs list thread, along with the solution. I hope someone at Atari or Firaxis will read this and correct this issue in the next (beta, or first official) patch.
Now to FINALLY play the game!