Kinda not the right place, but somewhat appropriate, so no worries.
The shift is probably caused by a refresh rate change. All you need to do is find the refresh rate of your monitor (right click on the desktop, click "Properties", "Settings", "Advanced" and "Monitor"). Then open your .ini file in the directory of the game you're trying to play, (civ3.ini, PTW.ini, conquests.ini) and add the line Refresh=XX, where XX is the refresh rate you saw in the Monitor tab.
Re: Rep...basically, if you can't do a GPT deal, your rep is trashed.