Ok - I'm guessing ptarth is going to post something in more detail later, but yes, this bug apparently does exist. It is reproducible and it is based on map control. I made quite a few tests with irek to confirm and yup, it happens. The issue occurs, without a doubt, between the russian and us versions of the game. That's the reason why I could never reproduce the bug - it doesn't appear to exist in US to US games.
So - here's the basics on how it happens.
At least 1 user has a US copy of the game. At least 1 user has a Russian copy of the game.
1 team takes all of the flags. The other team reclaims 1 flag. Boom. Invalid game state. It seemed to happen almost immediately when the forces of light are the team that is taking all of the flags. If forces of dark took all of the flags, then light took 1, it didn't always happen immediately. Sometimes swap the flags a few times.
I tested this with irek using a map that ptarth created that moves all flags to middle of the map. Once that triggered invalid gamestates consistently, we played an unmodified cataract and the invalid gamestate still occurs (i was light - took all flags, then irek, on dark, took 1 flag).
So, its reproducible. As far as a precise fix, something is probably off in the Russian localization file. Its unclear whether or not Russian v Russian games will have the same problem or not (but I'd think so).