Seems to desync in any and all modes of network setup if you use the online multiplayer system. At first I forwarded specific ports with alloy on and off, then did DMZ with alloy on and off. Desyncs every time.
Then we did direct connect with DMZ (as direct connect does not work with manual ports for some reason, only 6112). It was fine almost all the time. Then we had a third friend join in and after he finished download. After about a hour or two into the game ONLY HE desynced.
We saved game, had him delete Ironclad Games in My documents, then I zipped and gave him MY save. Loaded up fine and we finished the game with no desyncs.
Looks like desyncs arnt fixed when you reload game as you saved the desync itself. If the other players delete their save and grab the hosts or one other persons save thats desirable, it seems to work fine.