I've experienced this issue too. I have had a game with just the Iridium (the Trading Race) left on the map. I couldn't invade them for like the entire game. I ended up winning only because of influence and turning them that way (I had killed all the other opponents about 30 turns earlier).

Another game I was in, I couldn't invade two separate races. One of them was very powerful and in a good position, but with practically no defenses. The best play would have been to attack them / take over their position, but I couldn't invade them at all. Definitely annoying!

That sounds like a bug. I recall your prior post. I would submit the save. The only game options would be the 50 turn pragmatic cease to war followed by the UP declaration of peace. It is possible I suppose. You can check the UP screen to see if the war ban is current. Another possibility is that your starting the game teamed up with the AI? That would prevent any aggression for the entire game as your treated as allies forever.