Everything seems to work great for me except when I bought Nuclear Missiles. After buying them for use, they do NOT show up as an option to use in ship building.
Outside of that everything else works.
Please let me know how I can use them!
Nuclear Missiles are a race-specific weapon, they are only available to the Order. So in the ship design screen, select one of the Order’s cruiser hulls and then go to the weapons tab and you should find the nuclear missiles.
My brother had this same problem when he first tried the game, I wonder if the racial restrictions could be a bit more obvious on the fleet hq screen.