Seconding this. We (Three to four players, ~15 AI empires, 1 advanced, 1 FE, 3 Marauders, Huge 2-arm galaxy) noticed the first desync appearing when one of us upgraded to cyborgs. After that, it popped another time when there were species modified and once more when another player went psionic. We kept going on until the 2330s, where the desync issue began popping up more frequently. By now, it's literally impossible to play for longer than a few months before the desync happens again. This is feeling a little like the Utopia-Desync problem.
As of now, Multiplayer is seriously unplayable because of it.
As of now, Multiplayer is seriously unplayable because of it.