I too ran into the bizarre problem of sync bugs playing with my brother a couple of months ago over the break. It was bizarre, as though we were in some ways still in the same game, it was like we were playing out 'alternate universe' histories of what happened. Could have been interesting as a feature of some 'quantum probability' feuture -- but as it was in actual fact an irritating bug that had no off buttom and seemed to happen every game it really ruins the multiplayer experience.
I hadn't wrote on this yet because I had figured they would have gotten around to fixing it in one of the patches since December -- apparently not (I haven't been able to test this for months now, being too far away to coordinate a long-term game -- and aren't all sins games long-term games?).
If you could send the dev's some saved games (I sure don't have any at this point), I am sure it would be useful to them for solving the problem (maybe even sending both your save and your brother's?).
Hopefully this problem will be resolved shortly. Just one quick question though: I experienced this playing over a LAN, as i assume that Valkajin did.. have any of yee online players had the same problem?