Yeah, there's an issue where after a certain amouint happens the game basically stops tracking it. It exists in the original game, as well as any mods, however in some mods more is able to happen than in others; EaW was dealing with significantly fewer planets and factions, which made it much rarer. There is, as far as anyone has ever found, no way to fix it through modding. The only way would be if PG/LA decided to fix it through an official patch, which they won't.