are you guys playing the unpatched game by any chance?
I encountered smth similar, maybe even exactly the same, don't recall, but the point is that I had +4 in captured cities and +2 in my own
this was a long time ago, I even made a bug thread about it, and later it was fixed, at least according to the change logs
this might be smth different, or maybe both of you play the unpatched game by some weird coincidence