Custom race configuration does not save, so when you finish a game and go to start another you have to reset all the values. Not all that difficult to do, but it's driving me nuts mostly because I tend to play small map games. Did this in both 1.2 and 1.3B1.
There was what seemed to be a related problem with random settings not changing unless you reselected random at each new game startup, but that one looks to have been fixed in 1.3B1.
Oh, I know there is a work-around by editing the file name which essentially sets the custom race values to a new default.
Great game, loving the AI updates, and
thank you for fixing the planet invasion/flipping bug where the neutral PQ bonus would not apply correctly. Off to start another game.