I've had something like this problem too, and it still happens when I turn all other mods off. I've tested it somewhat and found that it will happen with Congessional Republics but not Liberal Democracies. My problem is slightly different in that it creates a bunch of parties at the very beginning (including Xeno/Anti-Xeno factions before alien contact) and does so every year or so or less. It gets very annoying and it pretty much breaks the game.