You didn't mention scores did you? You wouldn't by chance be over the mega evil empire threshold? But I have seen this behavior before in races when you weren't above the threshold, so that's just a thought.
As far as modding the file related to this behavior is the AI_anger file. You can try playing around with that and see what effect it has. I wouldn't get your hopes up though. Chances are good if you do manage to get them to pake peace you will end up with an ai race that is a pushover.
The AI are incapable of determining when an ally is preparing to stab them in the back, so to give them some chance at survival they need to be on the side of distrust I think. I hope this one factor isn't what you paid for when you bought the game.
The easiest way to end a war with an AI race is to exterminate them.
Geoschmo