While playing online multiplayer, we are experiencing a "different" kind of out of sync. The setup is using a custom map created in Map Designer (~100 planets and 4 players...) and when launched there are two humans and two AI
What seemingly happens is that the game goes out of sync after some period of time but it's not apparent and there is no typical minidump, the game just continues on except that each of the human players is effectively playing a seperate, different game.
We can communicate via the return key and game saves "show up" on each side, but when we "meet" at the same planet (audio communicating via phone...) he wont see my fleet and I wont see his fleet. In some cases we both are able to colonize the same planet and build it up. (It initially led to some interesting arguments about who had what planet(s) with each of us trying to tell the other that they couldn't read planet names...)
Again, when the game gets out of sync like this, we can still communicate within the game, each of us sees any gamesaves that are initiated and there is no apparent crash. The first game this happened in we happily spent ~6 hours playing along (it's a very large world, and we were on opposite sides...) fighting along with the AI and eventually figured out that we had occupied the same space and time but never run into each other, only AI...
There's nothing like spending that many hours getting ready to crush your pitifull excuse of a buddy and then find out he's not even there... 
help...