Sadly Rayadrel, Magnumaniac's reply #8 almost certainly sums up what is going on. You can't just be beating the AI, you actually have to take the time to grind down their military rating... or they will stupidly stay at war with you, because they think they are winning. The only other option is if you ever offered a peace treaty and then attacked again shortly thereafter because....
Then it should also keep track of wars won, wars started, peace treaties offered, and peace treaties accepted.
It already does this, at least at a basic level. In DA they added the "--they don't trust us modifier", which you pick up if you offer a peace treaty in exchange for something (money, tech, planets) and then attack the defeated party again. At this point, the AI will not surrender to you no matter what, and if surrender options are enabled they will always choose to surrender to someone else.
Strange, because I hadn't actually ever made peace with anyone in the galaxy - every war was fought to the death. Some flag got set there in error.
Maybe, maybe not. There are several ways to pick up the "--they don't trust us" flag, not all related to peace treaties. But once that shows up on your relationship screen, forget about peace with that AI. Other ways that flag is set is if you ever attack someone you had a treaty with, or if the AI has decided that in one of your wars you used a "sneak attack" - taking lots of worlds in the first turn of a war.
If you still have that save game, check to see if you have that flag set for that race. If you don't, then I don't know what is going on there....
Hope that helps.