Yes, I noticed that, too. I'm not near my computer so I can't check but I believe it's due to my internet connection. Sometimes it gets severed and when the CGOS client tries to reconnect it can't because the server thinks that a second client is trying to connect.
One way to do it seems to be to keep track of who owned each point at the end of each playout. Apparently if a point is owned 90% or more by one color it's safe to assume that the ownership won't change anymore. This could then be used to calculate a "real" score. I have no idea however how many playouts need to be run for this to work. But maybe we could give it a try some time.
I saw that comment, yes. The Windows version seems to be more prone to those things, it seems.