This problem is different, but I don't want to start a new thread yet.
I played 4otm1 last night, up to about 1100BC or so. No problems. Didn't do anything else with my computer, loaded up the save to continue. Now, my computer is acting strange. In the game, I get a pop-up menu every time I select a unit. Clicking isn't enough, I have to choose 'select all' or whatever from the menu to select a unit. The keyboard does not respond, for instance, 'g' doesn't mean Go anymore, it has no effect at all. Function keys have no effect, I have to do everything by clicking through these menus.
What's worse, it isn't isolated to just Civ4. For example, in Windows Explorer, using the scroll bar now closes the window. There may be other problems that I haven't discovered. It doesn't look good at all! Have you heard of anything like this?