I'm not exactly "new" to the Sins experience, but I am fairly virgin with the lingo.

Having said that, I THINK I'm having a similar problem.  I was playing with my buddy last night, and during the first couple of minutes everything was fine, but after.... MAYBE 3-5 minutes both of our games seemed to turn into two completely different experiences.  Neither one of us lagged out, and we could both still use the in-game chat, but what I saw happening and what he saw happening were two completely different things.

This isn't the first time this has happened since we downloaded Diplomacy, but I'm not gonna lose too much sleep over it.  With any luck the Stardock boys will have this nonsense hammered out soon. 

If you getting the Desync you need to be sending your Desync logs to IC. Not just your but everyone you desync with.

Here is how to enable the logs : Log Info

Also there is a seperate exe for Entrechment that will give more info for the Devs to track the bug: Desync Exe

Blair has also said in another post I cant find atm, that he has set aside time,money,and manpower to fix the bug once they find it, but it requires everyone who desyncs to enable their logs and send them in!