I have experienced the same problem. I posted a thread about it: cf. "Old problem . . ." However, no one has responded. This appeared in one of the earlier beta releases. I did find a "work-around" for the time being, but I do hope it is fixed. What I have done to get my leader's name and my choice of political party involves a couple steps.

First, go through the start-up screens making the choices of political party, abilities, ship colors, and leader names.

Second, allow the game to start. You will have Alan Bradley and the Federalist party. Without exiting the game, select the top left menu button.

Third, with the menu buttons on the bottom of the screen, go to Main Menu, and then select New Game. This time your choices should be preserved, and you should play with your party, leader, and all other choices.

It's a bit involved. There may be other work-arounds, but I could not discover a simpler way to get the party I wanted.

Good luck! I do hope they fix this!

P.S. I also experienced your surrender experience from another post.

On Beta 4C and 4D the game does not save or use many changes to the setup windows for a fresh game. The changes should be saved in the prefs.ini but they are not. Since the prefs.ini was moved to the "my games" folder on 4C I suspect there are some matching coding changes that were missed.