Hey, I have seen some desyncs too. It seems like people who don't restart their clients between games, or have played a couple games already without restarting, are more likely to go out of sync with those of us who do. Not sure if that helps. The desync eventually leads to a crash.
When everyone has just logged on or restarted their clients, I haven't seen a desync. A lot of us are in the habit of restarting, because this 95% protected against crashes in earlier versions.
I had one of my opponents send me their saved game...I was going to look at it, but it is kind of a drag without speed controls. Would it help to send someone my version and their version of the same game?
Otherwise, to try and capture the error, have one person never restart his client and the other person restart between each game. And play larger games with multiple players and maybe an AI thrown in. It seems more common on bigger games.