Hm I have an interesting... observation if you will.
So I tried the synrar file from Blair's post earlier with my friend. We've noticed this: It gives us a desync error right at the beginning of the game if we "restart" the game.
steps we did:
launch Sins entrenchment
log onto ironclad
one of us Host a game, set it up
start
look around the map, didn't like our starting positions, both of us quit the game
back to chat room, host another game, set it up,
start
We will get the "xxx player has been desync'd" whatever message as soon as the load screen is gone. Everytime.
The screen dimmed and the "xxx player has desync" thing stays on the screen. What's weird though is that while the screen is dimmed with that error message, we seem to stay sync'd. I'd ask my friend to move his ships. He'd move them, and then tell me which and where he moved... and it matches up. Then I'd do the same with my ships. And he sees what I've moved as well. We didn't keep playing to see if we end up real desync later since the dimmed screen and the error message is very distracting. Perhaps a question for people who desynced... Was it a fresh game you started? Ie: hosting/joining first game after launching sins? Or did you "restart" or perhaps finished a game and joining another?
After this episode, my friend and I made a point that we will relaunch sins whenever we start a game just as a test. And once we started, we'll stick with whatever map position we're stuck with. So far, we've gone through 3 games without desync . Lots of "i just move xxx here.. do you see it?" "I just colonized xxx, do you see it too?" "how many colonies do I have?" paranoia though! 
We didn't keep the checksum from earlier... Although I'm pretty sure we should be able to replicate the process to get them if you want it.
