Could you be a little more specific on what exactly the differences are? It could be that you're both using different galaxy rotations (one might be viewing it from one angle, the other person might be viewing it from upside-down from that angle). Is this something that happens gradually over time, or does the game suddenly drastically change?

Best way to prevent desync is for everyone to close their game and restart the program before starting a new game.

even if they had just specifically gotten on the game to play together?

alright, what also happens is that, i save the game and it saves it on both players, however if we were to load both games individually, they would be different. i loaded the game at one time, and his game, even though it was different, out of sync it was at a different time, if you get what i mean. like i am at 45 minutes into the game and he is at 35 minutes into the game.

this has happened in both sins of a galactic empire and sacrifice of angels 2, however these mods dont change the game in that way and should not affect the saving of the game