Went to Create New Game. Selected Game and list of colors to choose from was populated accordingly. Then realized the game selected was not what I wanted. Selected correct game but list of colors didn't update to colors for that new game. New game wouldn't take old colors.

 There are a number of things you can change during a game but color is not one of them. Nonetheless, "New game" should take.. Not sure if you're using scenarios, but maybe you didn't unlock the appropriate section?? Been a while since I've played with the designer.. Are you using random placement? ..or perhaps do you have a custom initial set-up?  Just spit-balling possibilities here..

what board are you talking about?

Try refreshing the page. I just went to the Create New Game page and every time I selected a new board or new scenario it reset the color selection to the first color on the new list.