This is still happening for me on every game.
After some testing, I think it only happens to me. Even with my friends hosting, I desync, but sometimes others in the game don't.
Could it be because I have a fast machine? I have an i7-2600k with 16GB RAM. I've also turned off all virtual memory, and I know some bad programming sometimes depends on some virtual memory being present, even if you have plenty of physical memory. Just an idea.
Another tidbit is in a game with just one friend allied against two AI, we were completely in sync on everything except the location of my battleship and one of his capital ships. Both were the second capital ship built, and we never saw correctly where the other one was. I hope that can help some because this is getting very frustrating.
And I still think it would be very easy to add a button to the beta client that says "Send latest save game to Stardock", which does everything it's supposed to do.