Mystikmind is also correct about ctrl-N being a cause of a sudden unexplained loss of AI intelligence. He mentioned that this is fixed in the latest patch which is something I have no knowledge about one way or the other. In any case it's really no big deal since ctrl-N only saves you a click or two. If you feel the need to use ctrl-N you may as well just go back to the main screen and start a new game. Then you're guaranteed not to see this issue.
Actually i do not know if it is an official fix in the latest patch? All i know is that my game never used to reset AI intelligence until recently when it suddenly started doing it. Then when i installed the latest patch it stopped doing it, that's all i know!
As for going back to the main screen to start a new game, sounds easy, but that is a severe pain in the ass if you have to keep doing it allot - especially if your looking for a particular map geography in order to try a new strategy/experiment or somthing.